rsem: rsem.xml annotate

annotate rsem.xml @ 4:0fa0c1132a7b draft

planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 3f67b2cf90a5de9880c98a6e492c444a5c856275

author	artbio
date	Wed, 28 Mar 2018 10:43:28 -0400
parents	9c7c44935bf1
children	78a1909aca3e

rev	line source
4 0fa0c1132a7b planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 3f67b2cf90a5de9880c98a6e492c444a5c856275 artbio parents: 3 diff changeset	1 <tool id="rsem" name="RSEM" version="0.3.1">
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	2 <description></description>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	3 <macros>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	4 <import>macros.xml</import>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	5 </macros>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	6 <requirements>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	7 <requirement type="package" version="1.3.0">rsem</requirement>
1 f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	8 <requirement type="package" version="1.2.2=py27pl5.22.0_0">bowtie</requirement>
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	9 </requirements>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	10 <stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	11 <exit_code range="1:" level="warning" description="Tool exception" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	12 </stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	14 #if $job.select_job == "index":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	15 echo ${job.reference_name} " " \| tee $reference_file &&
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	16 mkdir $reference_file.files_path &&
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	17 rsem-prepare-reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	18 #if $job.polya.polya_use == 'add':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	19 #if $job.polya.polya_length:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	20 --polyA-length $job.polya.polya_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	21 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	22 #elif $job.polya.polya_use == 'subset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	23 --no-polyA-subset $job.polya.no_polya_subset
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	24 #if $job.polya.polya_length:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	25 --polyA-length $job.polya.polya_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	26 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	27 #elif $job.polya.polya_use == 'none':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	28 --no-polyA
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	29 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	30 $job.ntog
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	31 #if $job.transcript_to_gene_map:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	32 --transcript-to-gene-map $job.transcript_to_gene_map
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	33 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	34 --bowtie
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	35 #if $job.self_reference.ref_type == 'transcripts':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	36 $job.self_reference.reference_fasta_file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	37 #else:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	38 --gtf $job.self_reference.gtf
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	39 $job.self_reference.reference_fasta_file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	40 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	41 ${reference_file.files_path}/${job.reference_name}
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	42 > ${reference_file.files_path}/${job.reference_name}.log
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	43 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	44
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	45 #if $job.select_job == "index" and $run_rsem.select == "Yes":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	46 &&
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	47 #end if
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	48
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	49 #if $run_rsem.select == "Yes":
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	50 #if $run_rsem.input.fastq.matepair=="single":
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	51 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	52 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	53 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	54 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	55 #end if
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	56 #elif $run_rsem.input.fastq.matepair=="paired":
4 0fa0c1132a7b planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 3f67b2cf90a5de9880c98a6e492c444a5c856275 artbio parents: 3 diff changeset	57 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	58 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	59 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	60 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	61 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	62 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	63 #end if
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	64 #end if
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	65 rsem-calculate-expression
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	66 ## --tag string
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	67 #if $run_rsem.seedlength:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	68 --seed-length $run_rsem.seedlength
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	69 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	70 --forward-prob $run_rsem.forward_prob
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	71 #if $run_rsem.rsem_options.fullparams == 'fullset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	72 ## Fragment info
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	73 #if $run_rsem.rsem_options.fragment_length_mean:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	74 --fragment-length-mean $run_rsem.rsem_options.fragment_length_mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	75 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	76 #if $run_rsem.rsem_options.fragment_length_min:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	77 --fragment-length-min $run_rsem.rsem_options.fragment_length_min
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	78 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	79 #if $run_rsem.rsem_options.fragment_length_sd:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	80 --fragment-length-sd $run_rsem.rsem_options.fragment_length_sd
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	81 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	82 #if $run_rsem.rsem_options.fragment_length_max:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	83 --fragment-length-max $run_rsem.rsem_options.fragment_length_max
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	84 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	85 ## RSPD
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	86 #if $run_rsem.rsem_options.rspd.estimate == 'yes':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	87 --estimate-rspd
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	88 #if $run_rsem.rsem_options.rspd.num_rspd_bins:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	89 --num-rspd-bins $run_rsem.rsem_options.rspd.num_rspd_bins
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	90 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	91 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	92 ## Calculate 95% credibility intervals and posterior mean estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	93 #if $run_rsem.rsem_options.useci.ci == 'yes':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	94 --calc-ci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	95 #if $run_rsem.rsem_options.useci.cimem:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	96 --ci-memory $run_rsem.rsem_options.useci.cimem
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	97 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	98 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	99 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	100 --num-threads \${GALAXY_SLOTS:-4}
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	101 #if $run_rsem.input.format == 'fasta' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	102 ## Bowtie params
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	103 #if $run_rsem.input.bowtie_options.bowtie_e:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	104 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	105 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	106 #if $run_rsem.input.bowtie_options.bowtie_m:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	107 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	108 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	109 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	110 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	111 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	112 ## Bowtie params
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	113 #if $run_rsem.input.bowtie_options.bowtie_e:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	114 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	115 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	116 #if $run_rsem.input.bowtie_options.bowtie_m:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	117 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	118 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	119 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	120 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	121 ## Outputs
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	122 #if $run_rsem.rsem_outputs.result_bams == 'none':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	123 --no-bam-output
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	124 #else
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	125 --sort-bam-by-coordinate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	126 --output-genome-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	127 $run_rsem.rsem_outputs.sampling_for_bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	128 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	129 ## Input data
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	130 #if $run_rsem.input.format=="fastq"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	131 $run_rsem.input.fastq_select
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	132 #if $run_rsem.input.fastq.matepair=="single":
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	133 uncomp_single.fastq
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	134 #elif $run_rsem.input.fastq.matepair=="paired":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	135 --paired-end
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	136 uncomp_pair1.fastq
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	137 uncomp_pair2.fastq
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	138 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	139 #elif $run_rsem.input.format=="fasta"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	140 --no-qualities
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	141 #if $run_rsem.input.fasta.matepair=="single":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	142 $run_rsem.input.fasta.singlefasta
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	143 #elif $run_rsem.input.fasta.matepair=="paired":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	144 --paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	145 $run_rsem.input.fasta.fasta1
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	146 $run_rsem.input.fasta.fasta2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	147 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	148 #elif $run_rsem.input.format=="sam"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	149 #if $run_rsem.input.matepair=="paired":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	150 --paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	151 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	152 #if $run_rsem.input.rsem_sam._extension == 'sam':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	153 --sam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	154 #elif $run_rsem.input.rsem_sam._extension == 'bam':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	155 --bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	156 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	157 $run_rsem.input.rsem_sam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	158 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	159 ## RSEM reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	160 #if $run_rsem.reference.refSrc == 'history':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	161 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	162 #elif $run_rsem.reference.refSrc == 'self':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	163 ${reference_file.files_path}/${job.reference_name}
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	164 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	165 ## sample_name: use a hard coded name so we can pull out galaxy outputs
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	166 rsem_output
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	167 ## direct output into logfile
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	168 > $log
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	169 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	170 ]]></command>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	171
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	172 <inputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	173 <conditional name="job">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	174 <param name="select_job" type="select" label="rsem reference">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	175 <option value="index">Build rsem reference</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	176 <option value="no-index" selected="true">rsem reference available from history</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	177 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	178 <when value="index">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	179 <conditional name="self_reference">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	180 <param name="ref_type" type="select" label="Reference transcript source">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	181 <option value="transcripts">transcript fasta</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	182 <option value="genomic">reference genome and gtf</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	183 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	184 <when value="transcripts">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	185 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	186 help="The files should contain the sequences of transcripts."/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	187 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	188 <when value="genomic">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	189 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	190 help="The file should contain the sequence of an entire genome."/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	191 <param name="gtf" type="data" format="gtf" label="gtf"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	192 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	193 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	194 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	195 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	196 <help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	197 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	198 The map can be obtained from the UCSC table browser
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	199 group: Genes and Gene Prediction Tracks
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	200 table: knownIsoforms
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	201 Without a map:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	202 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	203 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	204 </help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	205 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	206 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	207 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	208 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	209 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	210 <conditional name="polya">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	211 <param name="polya_use" type="select" label="PolyA ">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	212 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	213 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	214 <option value="none">Do not add poly(A) tails to any transcripts</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	215 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	216 <when value="add">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	217 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	218 <validator type="in_range" message="must be positive " min="1"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	219 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	220 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	221 <when value="subset">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	222 <param name="no_polya_subset" type="data" format="tabular" optional="true" label="List of transcript IDs (one per line) that should should not have polyA tails added."/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	223 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	224 <validator type="in_range" message="must be positive " min="1"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	225 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	226 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	227 <when value="none"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	228 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	229 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowtie uses the automatic N to G conversion to align against all positions in the reference."/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	230 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	231 <when value="no-index">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	232 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	233 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	234
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	235 <conditional name="run_rsem">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	236 <param name="select" type="select" label="calculate expression with rsem">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	237 <option value="No">Just build rsem reference for latter rsem profiling</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	238 <option value="Yes" selected="true">profile expression with rsem</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	239 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	240 <when value="Yes">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	241 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	242 <conditional name="reference">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	243 <param name="refSrc" type="select" label="RSEM Reference Source">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	244 <option value="history">From your history</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	245 <option value="self">Prepare RSEM Reference with this tool</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	246 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	247 <when value="history">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	248 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	249 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	250 <when value="self">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	251 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	252 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	253 <conditional name="input">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	254 <param name="format" type="select" label="RSEM Input file type">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	255 <option value="fastq">FASTQ</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	256 <option value="fasta">FASTA</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	257 <option value="sam">SAM/BAM</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	258 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	259 <when value="fastq">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	260 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	261 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	262 <option value="--solexa-quals">solexa qualities</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	263 <option value="--phred64-quals">phred64 qualities</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	264 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	265 <conditional name="fastq">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	266 <param name="matepair" type="select" label="Library type">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	267 <option value="single">Single End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	268 <option value="paired">Paired End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	269 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	270 <when value="single">
1 f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	271 <param name="singlefastq" type="data" format="fastq,fastq.gz" label="FASTQ file" />
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	272 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	273 <when value="paired">
1 f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	274 <param name="fastq1" type="data" format="fastq,fastq.gz" label="Read 1 fastq file" />
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	275 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Read 2 fastq file" />
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	276 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	277 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	278 <expand macro="bowtie_options"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	279 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	280 <when value="fasta">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	281 <conditional name="fasta">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	282 <param name="matepair" type="select" label="Library Type">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	283 <option value="single">Single End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	284 <option value="paired">Paired End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	285 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	286 <when value="single">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	287 <param name="singlefasta" type="data" format="fasta" label="fasta file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	288 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	289 <when value="paired">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	290 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	291 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	292 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	293 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	294 <expand macro="bowtie_options"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	295 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	296 <when value="sam">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	297 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	298 <param name="matepair" type="select" label="Library Type">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	299 <option value="single">Single End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	300 <option value="paired">Paired End Reads</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	301 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	302 <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	303 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	304 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	305 <expand macro="rsem_options"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	306 <conditional name="rsem_outputs">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	307 <param name="result_bams" type="select" label="Create bam results files"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	308 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	309 <option value="none">No BAM results files</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	310 <option value="default" selected="true">Transcript BAM results file</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	311 <option value="both">Transcript and genome BAM results files</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	312 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	313 <when value="none"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	314 <when value="default">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	315 <expand macro="sampling_for_bam"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	316 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	317 <when value="both">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	318 <expand macro="sampling_for_bam"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	319 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	320 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	321 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	322 <when value="No">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	323 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	324 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	325 </inputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	326
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	327 <outputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	328 <data format="rsem_ref" name="reference_file" label="RSEM ${job.reference_name} reference">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	329 <filter>job['select_job'] == "index"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	330 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	331 <data format="tabular" name="gene_abundances" label="${run_rsem.sample}.gene_abundances" from_work_dir="rsem_output.genes.results">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	332 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	333 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	334 <data format="tabular" name="isoform_abundances" label="${run_rsem.sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	335 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	336 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	337 <data format="bam" name="transcript_sorted_bam" label="${run_rsem.sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	338 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	339 <filter>rsem_outputs['result_bams'] != "none"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	340 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	341 <data format="bam" name="genome_sorted_bam" label="${run_rsem.sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	342 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	343 <filter>rsem_outputs['result_bams'] == "both"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	344 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	345 <data format="txt" name="log" label="${run_rsem.sample}.rsem_log">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	346 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	347 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	348 </outputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	349
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	350 <tests>
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	351 <test>
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	352 <param name="select_job" value="index"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	353 <param name="ref_type" value="genomic"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	354 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	355 <param name="gtf" value="ref.gtf" ftype="gtf"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	356 <param name="reference_name" value="ref"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	357 <param name="select" value="Yes"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	358 <param name="sample" value="rsem_sample"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	359 <param name="refSrc" value="self"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	360 <param name="format" value="fastq"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	361 <param name="matepair" value="single"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	362 <param name="singlefastq" value="test.fq" ftype="fastqsanger"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	363 <param name="result_bams" value="none"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	364 <output name="reference_file">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	365 <assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	366 <has_text text="ref" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	367 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	368 </output>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	369 <output name="gene_abundances" value="gene_abundances.tab"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	370 <output name="isoform_abundances" value="isoform_abundances.tab" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	371 <output name="log">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	372 <assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	373 <has_text text="Expression Results are written" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	374 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	375 </output>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	376 </test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	377 <test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	378 <param name="select_job" value="index"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	379 <param name="ref_type" value="genomic"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	380 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	381 <param name="gtf" value="ref.gtf" ftype="gtf"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	382 <param name="reference_name" value="ref"/>
1 f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	383 <param name="select" value="Yes"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	384 <param name="sample" value="rsem_sample"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	385 <param name="refSrc" value="self"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	386 <param name="format" value="fastq"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	387 <param name="matepair" value="single"/>
3 9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22 artbio parents: 2 diff changeset	388 <param name="singlefastq" value="test.fastq.gz" ftype="fastqsanger.gz"/>
1 f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	389 <param name="result_bams" value="none"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	390 <output name="reference_file">
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	391 <assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	392 <has_text text="ref" />
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	393 </assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	394 </output>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	395 <output name="gene_abundances" value="gene_abundances.tab"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	396 <output name="isoform_abundances" value="isoform_abundances.tab" />
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	397 <output name="log">
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	398 <assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	399 <has_text text="Expression Results are written" />
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	400 </assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	401 </output>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	402 </test>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	403 <test>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	404 <param name="select_job" value="index"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	405 <param name="ref_type" value="genomic"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	406 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	407 <param name="gtf" value="ref.gtf" ftype="gtf"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b artbio parents: 0 diff changeset	408 <param name="reference_name" value="ref"/>
0 8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	409 <param name="select" value="No"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	410 <output name="reference_file">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	411 <assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	412 <has_text text="ref" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	413 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	414 </output>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	415 </test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	416 </tests>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	417
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	418 <help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	419
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	420 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	421
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	422 NAME
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	423 rsem-prepare-reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	424
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	425 SYNOPSIS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	426 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	427
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	428 DESCRIPTION
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	429 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	430 This program is used in conjunction with the 'rsem-calculate-expression' program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	431
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	432 INPUTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	433 A fasta file of transcripts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	434 or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	435 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	436
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	437 ---
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	438
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	439 NAME
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	440 rsem-calculate-expression - Estimate gene and isoform expression from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	441 RNA-Seq data.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	442
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	443 SYNOPSIS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	444 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	445 rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	446 rsem-calculate-expression [options] --alignments [--paired-end] input reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	447
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	448 ARGUMENTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	449 upstream_read_files(s)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	450 Comma-separated list of files containing single-end reads or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	451 upstream reads for paired-end data. By default, these files are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	452 assumed to be in FASTQ format. If the --no-qualities option is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	453 specified, then FASTA format is expected.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	454
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	455 downstream_read_file(s)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	456 Comma-separated list of files containing downstream reads which are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	457 paired with the upstream reads. By default, these files are assumed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	458 to be in FASTQ format. If the --no-qualities option is specified,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	459 then FASTA format is expected.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	460
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	461 input
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	462 SAM/BAM/CRAM formatted input file. If "-" is specified for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	463 filename, the input is instead assumed to come from standard input.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	464 RSEM requires all alignments of the same read group together. For
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	465 paired-end reads, RSEM also requires the two mates of any alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	466 be adjacent. In addition, RSEM does not allow the SEQ and QUAL
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	467 fields to be empty. See Description section for how to make input
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	468 file obey RSEM's requirements.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	469
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	470 reference_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	471 The name of the reference used. The user must have run
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	472 'rsem-prepare-reference' with this reference_name before running
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	473 this program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	474
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	475 sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	476 The name of the sample analyzed. All output files are prefixed by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	477 this name (e.g., sample_name.genes.results)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	478
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	479 BASIC OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	480 --paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	481 Input reads are paired-end reads. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	482
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	483 --no-qualities
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	484 Input reads do not contain quality scores. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	485
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	486 --strandedness <none\|forward\|reverse>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	487 This option defines the strandedness of the RNA-Seq reads. It
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	488 recognizes three values: 'none', 'forward', and 'reverse'. 'none'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	489 refers to non-strand-specific protocols. 'forward' means all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	490 (upstream) reads are derived from the forward strand. 'reverse'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	491 means all (upstream) reads are derived from the reverse strand. If
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	492 'forward'/'reverse' is set, the '--norc'/'--nofw' Bowtie/Bowtie 2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	493 option will also be enabled to avoid aligning reads to the opposite
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	494 strand. For Illumina TruSeq Stranded protocols, please use
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	495 'reverse'. (Default: 'none')
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	496
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	497 -p/--num-threads <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	498 Number of threads to use. Both Bowtie/Bowtie2, expression estimation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	499 and 'samtools sort' will use this many threads. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	500
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	501 --alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	502 Input file contains alignments in SAM/BAM/CRAM format. The exact
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	503 file format will be determined automatically. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	504
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	505 --fai <file>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	506 If the header section of input alignment file does not contain
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	507 reference sequence information, this option should be turned on.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	508 <file> is a FAI format file containing each reference sequence's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	509 name and length. Please refer to the SAM official website for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	510 details of FAI format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	511
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	512 --bowtie2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	513 Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	514 does not handle indel, local and discordant alignments, the Bowtie2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	515 parameters are set in a way to avoid those alignments. In
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	516 particular, we use options '--sensitive --dpad 0 --gbar 99999999
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	517 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. The last parameter
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	518 of '--score-min', '-0.1', is the negative of maximum mismatch rate.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	519 This rate can be set by option '--bowtie2-mismatch-rate'. If reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	520 are paired-end, we additionally use options '--no-mixed' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	521 '--no-discordant'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	522
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	523 --star
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	524 Use STAR to align reads. Alignment parameters are from ENCODE3's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	525 STAR-RSEM pipeline. To save computational time and memory resources,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	526 STAR's Output BAM file is unsorted. It is stored in RSEM's temporary
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	527 directory with name as 'sample_name.bam'. Each STAR job will have
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	528 its own private copy of the genome in memory. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	529
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	530 --append-names
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	531 If gene_name/transcript_name is available, append it to the end of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	532 gene_id/transcript_id (separated by '_') in files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	533 'sample_name.isoforms.results' and 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	534 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	535
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	536 --seed <uint32>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	537 Set the seed for the random number generators used in calculating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	538 posterior mean estimates and credibility intervals. The seed must be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	539 a non-negative 32 bit integer. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	540
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	541 --single-cell-prior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	542 By default, RSEM uses Dirichlet(1) as the prior to calculate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	543 posterior mean estimates and credibility intervals. However, much
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	544 less genes are expressed in single cell RNA-Seq data. Thus, if you
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	545 want to compute posterior mean estimates and/or credibility
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	546 intervals and you have single-cell RNA-Seq data, you are recommended
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	547 to turn on this option. Then RSEM will use Dirichlet(0.1) as the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	548 prior which encourage the sparsity of the expression levels.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	549 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	550
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	551 --calc-pme
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	552 Run RSEM's collapsed Gibbs sampler to calculate posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	553 estimates. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	554
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	555 --calc-ci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	556 Calculate 95% credibility intervals and posterior mean estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	557 The credibility level can be changed by setting
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	558 '--ci-credibility-level'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	559
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	560 -q/--quiet
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	561 Suppress the output of logging information. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	562
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	563 -h/--help
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	564 Show help information.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	565
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	566 --version
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	567 Show version information.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	568
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	569 OUTPUT OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	570 --sort-bam-by-read-name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	571 Sort BAM file aligned under transcript coordidate by read name.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	572 Setting this option on will produce deterministic maximum likelihood
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	573 estimations from independent runs. Note that sorting will take long
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	574 time and lots of memory. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	575
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	576 --no-bam-output
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	577 Do not output any BAM file. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	578
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	579 --sampling-for-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	580 When RSEM generates a BAM file, instead of outputting all alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	581 a read has with their posterior probabilities, one alignment is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	582 sampled according to the posterior probabilities. The sampling
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	583 procedure includes the alignment to the "noise" transcript, which
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	584 does not appear in the BAM file. Only the sampled alignment has a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	585 weight of 1. All other alignments have weight 0. If the "noise"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	586 transcript is sampled, all alignments appeared in the BAM file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	587 should have weight 0. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	588
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	589 --output-genome-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	590 Generate a BAM file, 'sample_name.genome.bam', with alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	591 mapped to genomic coordinates and annotated with their posterior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	592 probabilities. In addition, RSEM will call samtools (included in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	593 RSEM package) to sort and index the bam file.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	594 'sample_name.genome.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	595 'sample_name.genome.sorted.bam.bai' will be generated. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	596 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	597
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	598 --sort-bam-by-coordinate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	599 Sort RSEM generated transcript and genome BAM files by coordinates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	600 and build associated indices. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	601
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	602 --sort-bam-memory-per-thread <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	603 Set the maximum memory per thread that can be used by 'samtools
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	604 sort'. <string> represents the memory and accepts suffices 'K/M/G'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	605 RSEM will pass <string> to the '-m' option of 'samtools sort'. Note
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	606 that the default used here is different from the default used by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	607 samtools. (Default: 1G)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	608
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	609 ALIGNER OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	610 --seed-length <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	611 Seed length used by the read aligner. Providing the correct value is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	612 important for RSEM. If RSEM runs Bowtie, it uses this value for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	613 Bowtie's seed length parameter. Any read with its or at least one of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	614 its mates' (for paired-end reads) length less than this value will
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	615 be ignored. If the references are not added poly(A) tails, the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	616 minimum allowed value is 5, otherwise, the minimum allowed value is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	617 25. Note that this script will only check if the value >= 5 and give
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	618 a warning message if the value < 25 but >= 5. (Default: 25)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	619
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	620 --phred33-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	621 Input quality scores are encoded as Phred+33. (Default: on)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	622
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	623 --phred64-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	624 Input quality scores are encoded as Phred+64 (default for GA
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	625 Pipeline ver. >= 1.3). (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	626
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	627 --solexa-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	628 Input quality scores are solexa encoded (from GA Pipeline ver. <
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	629 1.3). (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	630
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	631 --bowtie-path <path>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	632 The path to the Bowtie executables. (Default: the path to the Bowtie
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	633 executables is assumed to be in the user's PATH environment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	634 variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	635
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	636 --bowtie-n <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	637 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	638 Default: 2)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	639
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	640 --bowtie-e <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	641 (Bowtie parameter) max sum of mismatch quality scores across the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	642 alignment. (Default: 99999999)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	643
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	644 --bowtie-m <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	645 (Bowtie parameter) suppress all alignments for a read if > <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	646 valid alignments exist. (Default: 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	647
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	648 --bowtie-chunkmbs <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	649 (Bowtie parameter) memory allocated for best first alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	650 calculation (Default: 0 - use Bowtie's default)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	651
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	652 --bowtie2-path <path>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	653 (Bowtie 2 parameter) The path to the Bowtie 2 executables. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	654 the path to the Bowtie 2 executables is assumed to be in the user's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	655 PATH environment variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	656
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	657 --bowtie2-mismatch-rate <double>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	658 (Bowtie 2 parameter) The maximum mismatch rate allowed. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	659 0.1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	660
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	661 --bowtie2-k <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	662 (Bowtie 2 parameter) Find up to <int> alignments per read. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	663 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	664
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	665 --bowtie2-sensitivity-level <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	666 (Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	667 mode. This option controls how hard Bowtie 2 tries to find
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	668 alignments. <string> must be one of "very_fast", "fast", "sensitive"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	669 and "very_sensitive". The four candidates correspond to Bowtie 2's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	670 "--very-fast", "--fast", "--sensitive" and "--very-sensitive"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	671 options. (Default: "sensitive" - use Bowtie 2's default)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	672
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	673 --star-path <path>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	674 The path to STAR's executable. (Default: the path to STAR executable
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	675 is assumed to be in user's PATH environment variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	676
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	677 --star-gzipped-read-file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	678 (STAR parameter) Input read file(s) is compressed by gzip. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	679 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	680
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	681 --star-bzipped-read-file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	682 (STAR parameter) Input read file(s) is compressed by bzip2.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	683 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	684
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	685 --star-output-genome-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	686 (STAR parameter) Save the BAM file from STAR alignment under genomic
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	687 coordinate to 'sample_name.STAR.genome.bam'. This file is NOT sorted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	688 by genomic coordinate. In this file, according to STAR's manual,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	689 'paired ends of an alignment are always adjacent, and multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	690 alignments of a read are adjacent as well'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	691
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	692 ADVANCED OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	693 --tag <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	694 The name of the optional field used in the SAM input for identifying
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	695 a read with too many valid alignments. The field should have the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	696 format <tagName>:i:<value>, where a <value> bigger than 0 indicates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	697 a read with too many alignments. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	698
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	699 --fragment-length-min <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	700 Minimum read/insert length allowed. This is also the value for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	701 Bowtie/Bowtie2 -I option. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	702
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	703 --fragment-length-max <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	704 Maximum read/insert length allowed. This is also the value for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	705 Bowtie/Bowtie 2 -X option. (Default: 1000)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	706
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	707 --fragment-length-mean <double>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	708 (single-end data only) The mean of the fragment length distribution,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	709 which is assumed to be a Gaussian. (Default: -1, which disables use
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	710 of the fragment length distribution)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	711
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	712 --fragment-length-sd <double>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	713 (single-end data only) The standard deviation of the fragment length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	714 distribution, which is assumed to be a Gaussian. (Default: 0, which
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	715 assumes that all fragments are of the same length, given by the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	716 rounded value of --fragment-length-mean)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	717
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	718 --estimate-rspd
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	719 Set this option if you want to estimate the read start position
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	720 distribution (RSPD) from data. Otherwise, RSEM will use a uniform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	721 RSPD. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	722
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	723 --num-rspd-bins <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	724 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	725 specified. Use of the default setting is recommended. (Default: 20)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	726
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	727 --gibbs-burnin <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	728 The number of burn-in rounds for RSEM's Gibbs sampler. Each round
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	729 passes over the entire data set once. If RSEM can use multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	730 threads, multiple Gibbs samplers will start at the same time and all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	731 samplers share the same burn-in number. (Default: 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	732
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	733 --gibbs-number-of-samples <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	734 The total number of count vectors RSEM will collect from its Gibbs
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	735 samplers. (Default: 1000)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	736
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	737 --gibbs-sampling-gap <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	738 The number of rounds between two succinct count vectors RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	739 collects. If the count vector after round N is collected, the count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	740 vector after round N + <int> will also be collected. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	741
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	742 --ci-credibility-level <double>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	743 The credibility level for credibility intervals. (Default: 0.95)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	744
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	745 --ci-memory <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	746 Maximum size (in memory, MB) of the auxiliary buffer used for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	747 computing credibility intervals (CI). (Default: 1024)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	748
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	749 --ci-number-of-samples-per-count-vector <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	750 The number of read generating probability vectors sampled per
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	751 sampled count vector. The crebility intervals are calculated by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	752 first sampling P(C \| D) and then sampling P(Theta \| C) for each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	753 sampled count vector. This option controls how many Theta vectors
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	754 are sampled per sampled count vector. (Default: 50)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	755
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	756 --keep-intermediate-files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	757 Keep temporary files generated by RSEM. RSEM creates a temporary
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	758 directory, 'sample_name.temp', into which it puts all intermediate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	759 output files. If this directory already exists, RSEM overwrites all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	760 files generated by previous RSEM runs inside of it. By default,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	761 after RSEM finishes, the temporary directory is deleted. Set this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	762 option to prevent the deletion of this directory and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	763 intermediate files inside of it. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	764
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	765 --temporary-folder <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	766 Set where to put the temporary files generated by RSEM. If the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	767 folder specified does not exist, RSEM will try to create it.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	768 (Default: sample_name.temp)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	769
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	770 --time
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	771 Output time consumed by each step of RSEM to 'sample_name.time'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	772 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	773
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	774 PRIOR-ENHANCED RSEM OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	775 --run-pRSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	776 Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	777 isoform's initial pseudo-count for RSEM's Gibbs sampling, will be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	778 learned from input RNA-seq data and an external data set. When pRSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	779 needs and only needs ChIP-seq peak information to partition isoforms
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	780 (e.g. in pRSEM's default partition model), either ChIP-seq peak file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	781 (with the '--chipseq-peak-file' option) or ChIP-seq FASTQ files for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	782 target and input and the path for Bowtie executables are required
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	783 (with the '--chipseq-target-read-files <string>',
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	784 '--chipseq-control-read-files <string>', and '--bowtie-path <path>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	785 options), otherwise, ChIP-seq FASTQ files for target and control and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	786 the path to Bowtie executables are required. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	787
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	788 --chipseq-peak-file <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	789 Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	790 BED6+4, format. This file is used when running prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	791 in the default two-partition model. It partitions isoforms by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	792 whether they have ChIP-seq overlapping with their transcription
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	793 start site region or not. Each partition will have its own prior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	794 parameter learned from a training set. This file can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	795 gzipped or ungzipped. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	796
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	797 --chipseq-target-read-files <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	798 Comma-separated full path of FASTQ read file(s) for ChIP-seq target.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	799 This option is used when running prior-enhanced RSEM. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	800 information to calculate ChIP-seq peaks and signals. The file(s) can
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	801 be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	802 options '--bowtie-path <path>' and '--chipseq-control-read-files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	803 <string>' must be defined when this option is specified. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	804 "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	805
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	806 --chipseq-control-read-files <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	807 Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	808 This option is used when running prior-enhanced RSEM. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	809 information to call ChIP-seq peaks. The file(s) can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	810 ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	811 '--bowtie-path <path>' and '--chipseq-target-read-files <string>'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	812 must be defined when this option is specified. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	813
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	814 --chipseq-read-files-multi-targets <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	815 Comma-separated full path of FASTQ read files for multiple ChIP-seq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	816 targets. This option is used when running prior-enhanced RSEM, where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	817 prior is learned from multiple complementary data sets. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	818 information to calculate ChIP-seq signals. All files can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	819 ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	820 option is specified, the option '--bowtie-path <path>' must be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	821 defined and the option '--partition-model <string>' will be set to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	822 'cmb_lgt' automatically. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	823
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	824 --chipseq-bed-files-multi-targets <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	825 Comma-separated full path of BED files for multiple ChIP-seq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	826 targets. This option is used when running prior-enhanced RSEM, where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	827 prior is learned from multiple complementary data sets. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	828 information of ChIP-seq signals and must have at least the first six
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	829 BED columns. All files can be either ungzipped or gzipped with a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	830 suffix '.gz' or '.gzip'. When this option is specified, the option
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	831 '--partition-model <string>' will be set to 'cmb_lgt' automatically.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	832 (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	833
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	834 --cap-stacked-chipseq-reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	835 Keep a maximum number of ChIP-seq reads that aligned to the same
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	836 genomic interval. This option is used when running prior-enhanced
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	837 RSEM, where prior is learned from multiple complementary data sets.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	838 This option is only in use when either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	839 '--chipseq-read-files-multi-targets <string>' or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	840 '--chipseq-bed-files-multi-targets <string>' is specified. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	841 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	842
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	843 --n-max-stacked-chipseq-reads <int>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	844 The maximum number of stacked ChIP-seq reads to keep. This option is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	845 used when running prior-enhanced RSEM, where prior is learned from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	846 multiple complementary data sets. This option is only in use when
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	847 the option '--cap-stacked-chipseq-reads' is set. (Default: 5)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	848
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	849 --partition-model <string>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	850 A keyword to specify the partition model used by prior-enhanced
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	851 RSEM. It must be one of the following keywords:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	852
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	853 - pk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	854 Partitioned by whether an isoform has a ChIP-seq peak overlapping
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	855 with its transcription start site (TSS) region. The TSS region is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	856 defined as [TSS-500bp, TSS+500bp]. For simplicity, we refer this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	857 type of peak as 'TSS peak' when explaining other keywords.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	858
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	859 - pk_lgtnopk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	860 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	861 peak' set, a logistic model is employed to further classify them
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	862 into two partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	863
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	864 - lm3, lm4, lm5, or lm6
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	865 Based on their ChIP-seq signals, isoforms are classified into 3,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	866 4, 5, or 6 partitions by a linear regression model.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	867
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	868 - nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	869 First partitioned by TSS peak. Then, for isoforms in the 'with TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	870 peak' set, a linear regression model is employed to further
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	871 classify them into 2, 3, 4, or 5 partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	872
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	873 - pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	874 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	875 peak' set, a linear regression model is employed to further
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	876 classify them into 2, 3, 4, or 5 partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	877
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	878 - cmb_lgt
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	879 Using a logistic regression to combine TSS signals from multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	880 complementary data sets and partition training set isoform into
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	881 'expressed' and 'not expressed'. This partition model is only in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	882 use when either '--chipseq-read-files-multi-targets <string>' or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	883 '--chipseq-bed-files-multi-targets <string> is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	884
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	885 Parameters for all the above models are learned from a training set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	886 For detailed explanations, please see prior-enhanced RSEM's paper.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	887 (Default: 'pk')
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	888
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	889 DEPRECATED OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	890 The options in this section are deprecated. They are here only for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	891 compatibility reasons and may be removed in future releases.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	892
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	893 --sam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	894 Inputs are alignments in SAM format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	895
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	896 --bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	897 Inputs are alignments in BAM format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	898
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	899 --strand-specific
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	900 Equivalent to '--strandedness forward'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	901
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	902 --forward-prob <double>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	903 Probability of generating a read from the forward strand of a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	904 transcript. Set to 1 for a strand-specific protocol where all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	905 (upstream) reads are derived from the forward strand, 0 for a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	906 strand-specific protocol where all (upstream) read are derived from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	907 the reverse strand, or 0.5 for a non-strand-specific protocol.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	908 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	909
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	910 DESCRIPTION
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	911 In its default mode, this program aligns input reads against a reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	912 transcriptome with Bowtie and calculates expression values using the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	913 alignments. RSEM assumes the data are single-end reads with quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	914 scores, unless the '--paired-end' or '--no-qualities' options are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	915 specified. Alternatively, users can use STAR to align reads using the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	916 '--star' option. RSEM has provided options in 'rsem-prepare-reference'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	917 to prepare STAR's genome indices. Users may use an alternative aligner
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	918 by specifying '--alignments', and providing an alignment file in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	919 SAM/BAM/CRAM format. However, users should make sure that they align
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	920 against the indices generated by 'rsem-prepare-reference' and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	921 alignment file satisfies the requirements mentioned in ARGUMENTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	922 section.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	923
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	924 One simple way to make the alignment file satisfying RSEM's requirements
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	925 is to use the 'convert-sam-for-rsem' script. This script accepts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	926 SAM/BAM/CRAM files as input and outputs a BAM file. For example, type
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	927 the following command to convert a SAM file, 'input.sam', to a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	928 ready-for-use BAM file, 'input_for_rsem.bam':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	929
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	930 convert-sam-for-rsem input.sam input_for_rsem
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	931
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	932 For details, please refer to 'convert-sam-for-rsem's documentation page.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	933
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	934 NOTES
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	935 1. Users must run 'rsem-prepare-reference' with the appropriate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	936 reference before using this program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	937
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	938 2. For single-end data, it is strongly recommended that the user provide
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	939 the fragment length distribution parameters (--fragment-length-mean and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	940 --fragment-length-sd). For paired-end data, RSEM will automatically
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	941 learn a fragment length distribution from the data.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	942
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	943 3. Some aligner parameters have default values different from their
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	944 original settings.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	945
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	946 4. With the '--calc-pme' option, posterior mean estimates will be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	947 calculated in addition to maximum likelihood estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	948
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	949 5. With the '--calc-ci' option, 95% credibility intervals and posterior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	950 mean estimates will be calculated in addition to maximum likelihood
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	951 estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	952
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	953 6. The temporary directory and all intermediate files will be removed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	954 when RSEM finishes unless '--keep-intermediate-files' is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	955
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	956 With the '--run-pRSEM' option and associated options (see section
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	957 'PRIOR-ENHANCED RSEM OPTIONS' above for details), prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	958 will be running. Prior parameters will be learned from supplied external
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	959 data set(s) and assigned as initial pseudo-counts for isoforms in the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	960 corresponding partition for Gibbs sampling.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	961
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	962 OUTPUT
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	963 sample_name.isoforms.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	964 File containing isoform level expression estimates. The first line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	965 contains column names separated by the tab character. The format of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	966 each line in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	967
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	968 transcript_id gene_id length effective_length expected_count TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	969 FPKM IsoPct [posterior_mean_count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	970 posterior_standard_deviation_of_count pme_TPM pme_FPKM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	971 IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	972 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	973 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	974
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	975 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	976 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	977 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	978
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	979 'transcript_id' is the transcript name of this transcript. 'gene_id'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	980 is the gene name of the gene which this transcript belongs to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	981 (denote this gene as its parent gene). If no gene information is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	982 provided, 'gene_id' and 'transcript_id' are the same.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	983
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	984 'length' is this transcript's sequence length (poly(A) tail is not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	985 counted). 'effective_length' counts only the positions that can
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	986 generate a valid fragment. If no poly(A) tail is added,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	987 'effective_length' is equal to transcript length - mean fragment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	988 length + 1. If one transcript's effective length is less than 1,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	989 this transcript's both effective length and abundance estimates are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	990 set to 0.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	991
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	992 'expected_count' is the sum of the posterior probability of each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	993 read comes from this transcript over all reads. Because 1) each read
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	994 aligning to this transcript has a probability of being generated
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	995 from background noise; 2) RSEM may filter some alignable low quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	996 reads, the sum of expected counts for all transcript are generally
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	997 less than the total number of reads aligned.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	998
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	999 'TPM' stands for Transcripts Per Million. It is a relative measure
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1000 of transcript abundance. The sum of all transcripts' TPM is 1
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1001 million. 'FPKM' stands for Fragments Per Kilobase of transcript per
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1002 Million mapped reads. It is another relative measure of transcript
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1003 abundance. If we define l_bar be the mean transcript length in a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1004 sample, which can be calculated as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1005
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1006 l_bar = \sum_i TPM_i / 10^6 * effective_length_i (i goes through
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1007 every transcript),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1008
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1009 the following equation is hold:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1010
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1011 FPKM_i = 10^3 / l_bar * TPM_i.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1012
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1013 We can see that the sum of FPKM is not a constant across samples.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1014
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1015 'IsoPct' stands for isoform percentage. It is the percentage of this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1016 transcript's abandunce over its parent gene's abandunce. If its
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1017 parent gene has only one isoform or the gene information is not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1018 provided, this field will be set to 100.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1019
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1020 'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1021 estimates calculated by RSEM's Gibbs sampler.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1022 'posterior_standard_deviation_of_count' is the posterior standard
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1023 deviation of counts. 'IsoPct_from_pme_TPM' is the isoform percentage
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1024 calculated from 'pme_TPM' values.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1025
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1026 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1027 and 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1028 credibility intervals for TPM and FPKM values. The bounds are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1029 inclusive (i.e. [l, u]).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1030
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1031 'TPM_coefficient_of_quartile_variation' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1032 'FPKM_coefficient_of_quartile_variation' are coefficients of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1033 quartile variation (CQV) for TPM and FPKM values. CQV is a robust
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1034 way of measuring the ratio between the standard deviation and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1035 mean. It is defined as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1036
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1037 CQV := (Q3 - Q1) / (Q3 + Q1),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1038
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1039 where Q1 and Q3 are the first and third quartiles.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1040
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1041 sample_name.genes.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1042 File containing gene level expression estimates. The first line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1043 contains column names separated by the tab character. The format of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1044 each line in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1045
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1046 gene_id transcript_id(s) length effective_length expected_count TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1047 FPKM [posterior_mean_count posterior_standard_deviation_of_count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1048 pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1049 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1050 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1051
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1052 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1053 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1054 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1055
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1056 'transcript_id(s)' is a comma-separated list of transcript_ids
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1057 belonging to this gene. If no gene information is provided,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1058 'gene_id' and 'transcript_id(s)' are identical (the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1059 'transcript_id').
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1060
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1061 A gene's 'length' and 'effective_length' are defined as the weighted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1062 average of its transcripts' lengths and effective lengths (weighted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1063 by 'IsoPct'). A gene's abundance estimates are just the sum of its
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1064 transcripts' abundance estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1065
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1066 sample_name.alleles.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1067 Only generated when the RSEM references are built with
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1068 allele-specific transcripts.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1069
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1070 This file contains allele level expression estimates for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1071 allele-specific expression calculation. The first line contains
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1072 column names separated by the tab character. The format of each line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1073 in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1074
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1075 allele_id transcript_id gene_id length effective_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1076 expected_count TPM FPKM AlleleIsoPct AlleleGenePct
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1077 [posterior_mean_count posterior_standard_deviation_of_count pme_TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1078 pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1079 TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1080 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1081 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1082
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1083 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1084 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1085 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1086
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1087 'allele_id' is the allele-specific name of this allele-specific
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1088 transcript.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1089
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1090 'AlleleIsoPct' stands for allele-specific percentage on isoform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1091 level. It is the percentage of this allele-specific transcript's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1092 abundance over its parent transcript's abundance. If its parent
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1093 transcript has only one allele variant form, this field will be set
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1094 to 100.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1095
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1096 'AlleleGenePct' stands for allele-specific percentage on gene level.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1097 It is the percentage of this allele-specific transcript's abundance
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1098 over its parent gene's abundance.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1099
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1100 'AlleleIsoPct_from_pme_TPM' and 'AlleleGenePct_from_pme_TPM' have
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1101 similar meanings. They are calculated based on posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1102 estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1103
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1104 Please note that if this file is present, the fields 'length' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1105 'effective_length' in 'sample_name.isoforms.results' should be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1106 interpreted similarly as the corresponding definitions in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1107 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1108
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1109 sample_name.transcript.bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1110 Only generated when --no-bam-output is not specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1111
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1112 'sample_name.transcript.bam' is a BAM-formatted file of read
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1113 alignments in transcript coordinates. The MAPQ field of each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1114 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1115 where w is the posterior probability of that alignment being the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1116 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1117 where value is a single precision floating number representing the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1118 posterior probability. Because this file contains all alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1119 lines produced by bowtie or user-specified aligners, it can also be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1120 used as a replacement of the aligner generated BAM/SAM file.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1121
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1122 sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1123 Only generated when --no-bam-output is not specified and --sort-bam-by-coordinate is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1124
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1125 'sample_name.transcript.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1126 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1127 indices generated by samtools (included in RSEM package).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1128
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1129 sample_name.genome.bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1130 Only generated when --no-bam-output is not specified and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1131 --output-genome-bam is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1132
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1133 'sample_name.genome.bam' is a BAM-formatted file of read alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1134 in genomic coordinates. Alignments of reads that have identical
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1135 genomic coordinates (i.e., alignments to different isoforms that
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1136 share the same genomic region) are collapsed into one alignment. The
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1137 MAPQ field of each alignment is set to min(100, floor(-10 *
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1138 log10(1.0 - w) + 0.5)), where w is the posterior probability of that
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1139 alignment being the true mapping of a read. In addition, RSEM pads a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1140 new tag ZW:f:value, where value is a single precision floating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1141 number representing the posterior probability. If an alignment is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1142 spliced, a XS:A:value tag is also added, where value is either '+'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1143 or '-' indicating the strand of the transcript it aligns to.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1144
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1145 sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1146 Only generated when --no-bam-output is not specified, and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1147 --sort-bam-by-coordinate and --output-genome-bam are specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1148
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1149 'sample_name.genome.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1150 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1151 indices generated by samtools (included in RSEM package).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1152
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1153 sample_name.time
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1154 Only generated when --time is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1155
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1156 It contains time (in seconds) consumed by aligning reads, estimating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1157 expression levels and calculating credibility intervals.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1158
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1159 sample_name.stat
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1160 This is a folder instead of a file. All model related statistics are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1161 stored in this folder. Use 'rsem-plot-model' can generate plots
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1162 using this folder.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1163
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1164 'sample_name.stat/sample_name.cnt' contains alignment statistics.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1165 The format and meanings of each field are described in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1166 'cnt_file_description.txt' under RSEM directory.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1167
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1168 'sample_name.stat/sample_name.model' stores RNA-Seq model parameters
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1169 learned from the data. The format and meanings of each filed of this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1170 file are described in 'model_file_description.txt' under RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1171 directory.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1172
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1173 The following four output files will be generated only by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1174 prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1175
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1176 - 'sample_name.stat/sample_name_prsem.all_tr_features'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1177 It stores isofrom features for deriving and assigning pRSEM prior.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1178 The first line is a header and the rest is one isoform per line.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1179 The description for each column is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1180
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1181 * trid: transcript ID from input annotation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1182
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1183 * geneid: gene ID from input anntation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1184
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1185 * chrom: isoform's chromosome name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1186
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1187 * strand: isoform's strand name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1188
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1189 * start: isoform's end with the lowest genomic loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1190
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1191 * end: isoform's end with the highest genomic loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1192
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1193 * tss_mpp: average mappability of [TSS-500bp, TSS+500bp], where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1194 TSS is isoform's transcription start site, i.e. 5'-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1195
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1196 * body_mpp: average mappability of (TSS+500bp, TES-500bp), where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1197 TES is isoform's transcription end site, i.e. 3'-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1198
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1199 * tes_mpp: average mappability of [TES-500bp, TES+500bp]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1200
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1201 * pme_count: isoform's fragment or read count from RSEM's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1202 posterior mean estimates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1203
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1204 * tss: isoform's TSS loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1205
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1206 * tss_pk: equal to 1 if isoform's [TSS-500bp, TSS+500bp] region
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1207 overlaps with a RNA Pol II peak; 0 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1208
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1209 * is_training: equal to 1 if isoform is in the training set where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1210 Pol II prior is learned; 0 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1211
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1212 - 'sample_name.stat/sample_name_prsem.all_tr_prior'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1213 It stores prior parameters for every isoform. This file does not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1214 have a header. Each line contains a prior parameter and an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1215 isoform's transcript ID delimited by " # ".
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1216
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1217 - 'sample_name.stat/sample_name_uniform_prior_1.isoforms.results'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1218 RSEM's posterior mean estimates on the isoform level with an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1219 initial pseudo-count of one for every isoform. It is in the same
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1220 format as the 'sample_name.isoforms.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1221
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1222 - 'sample_name.stat/sample_name_uniform_prior_1.genes.results'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1223 RSEM's posterior mean estimates on the gene level with an initial
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1224 pseudo-count of one for every isoform. It is in the same format as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1225 the 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1226
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1227 When learning prior from multiple external data sets in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1228 prior-enhanced RSEM, two additional output files will be generated.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1229
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1230 - 'sample_name.stat/sample_name.pval_LL'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1231 It stores a p-value and a log-likelihood. The p-value indicates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1232 whether the combination of multiple complementary data sets is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1233 informative for RNA-seq quantification. The log-likelihood shows
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1234 how well pRSEM's Dirichlet-multinomial model fits the read counts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1235 of partitioned training set isoforms.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1236
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1237 - 'sample_name.stat/sample_name.lgt_mdl.RData'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1238 It stores an R object named 'glmmdl', which is a logistic
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1239 regression model on the training set isoforms and multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1240 external data sets.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1241
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1242 In addition, extra columns will be added to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1243 'sample_name.stat/all_tr_features'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1244
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1245 * is_expr: equal to 1 if isoform has an abundance >= 1 TPM and a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1246 non-zero read count from RSEM's posterior mean estimates; 0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1247 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1248
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1249 * "$external_data_set_basename": log10 of external data's signal at
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1250 [TSS-500, TSS+500]. Signal is the number of reads aligned within
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1251 that interval and normalized to RPKM by read depth and interval
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1252 length. It will be set to -4 if no read aligned to that interval.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1253
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1254 There are multiple columns like this one, where each represents an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1255 external data set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1256
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1257 * prd_expr_prob: predicted probability from logistic regression
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1258 model on whether this isoform is expressed or not. A probability
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1259 higher than 0.5 is considered as expressed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1260
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1261 * partition: group index, to which this isoforms is partitioned
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1262
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1263 * prior: prior parameter for this isoform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1264
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1265 EXAMPLES
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1266 Assume the path to the bowtie executables is in the user's PATH
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1267 environment variable. Reference files are under '/ref' with name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1268 'mouse_125'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1269
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1270 1) '/data/mmliver.fq', single-end reads with quality scores. Quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1271 scores are encoded as for 'GA pipeline version >= 1.3'. We want to use 8
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1272 threads and generate a genome BAM file. In addition, we want to append
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1273 gene/transcript names to the result files:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1274
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1275 rsem-calculate-expression --phred64-quals \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1276 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1277 --append-names \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1278 --output-genome-bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1279 /data/mmliver.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1280 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1281 mmliver_single_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1282
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1283 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', stranded paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1284 reads with quality scores. Suppose the library is prepared using TruSeq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1285 Stranded Kit, which means the first mate should map to the reverse
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1286 strand. Quality scores are in SANGER format. We want to use 8 threads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1287 and do not generate a genome BAM file:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1288
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1289 rsem-calculate-expression -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1290 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1291 --strandedness reverse \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1292 /data/mmliver_1.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1293 /data/mmliver_2.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1294 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1295 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1296
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1297 3) '/data/mmliver.fa', single-end reads without quality scores. We want
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1298 to use 8 threads:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1299
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1300 rsem-calculate-expression -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1301 --no-qualities \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1302 /data/mmliver.fa \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1303 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1304 mmliver_single_without_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1305
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1306 4) Data are the same as 1). This time we assume the bowtie executables
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1307 are under '/sw/bowtie'. We want to take a fragment length distribution
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1308 into consideration. We set the fragment length mean to 150 and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1309 standard deviation to 35. In addition to a BAM file, we also want to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1310 generate credibility intervals. We allow RSEM to use 1GB of memory for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1311 CI calculation:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1312
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1313 rsem-calculate-expression --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1314 --phred64-quals \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1315 --fragment-length-mean 150.0 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1316 --fragment-length-sd 35.0 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1317 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1318 --output-genome-bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1319 --calc-ci \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1320 --ci-memory 1024 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1321 /data/mmliver.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1322 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1323 mmliver_single_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1324
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1325 5) '/data/mmliver_paired_end_quals.bam', BAM-formatted alignments for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1326 paired-end reads with quality scores. We want to use 8 threads:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1327
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1328 rsem-calculate-expression --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1329 --alignments \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1330 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1331 /data/mmliver_paired_end_quals.bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1332 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1333 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1334
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1335 6) '/data/mmliver_1.fq.gz' and '/data/mmliver_2.fq.gz', paired-end reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1336 with quality scores and read files are compressed by gzip. We want to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1337 use STAR to aligned reads and assume STAR executable is '/sw/STAR'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1338 Suppose we want to use 8 threads and do not generate a genome BAM file:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1339
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1340 rsem-calculate-expression --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1341 --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1342 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1343 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1344 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1345 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1346 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1347 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1348 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1349 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1350
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1351 7) In the above example, suppose we want to run prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1352 instead. Assuming we want to learn priors from a ChIP-seq peak file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1353 '/data/mmlive.narrowPeak.gz':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1354
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1355 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1356 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1357 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1358 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1359 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1360 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1361 --chipseq-peak-file /data/mmliver.narrowPeak.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1362 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1363 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1364 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1365 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1366 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1367
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1368 8) Similar to the example in 7), suppose we want to use the partition
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1369 model 'pk_lm2nopk' (partitioning isoforms by Pol II TSS peak first and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1370 then partitioning 'no TSS peak' isoforms into two bins by a linear
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1371 regression model), and we want to partition isoforms by RNA Pol II's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1372 ChIP-seq read files '/data/mmliver_PolIIRep1.fq.gz' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1373 '/data/mmliver_PolIIRep2.fq.gz', and the control ChIP-seq read files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1374 '/data/mmliver_ChIPseqCtrl.fq.gz'. Also, assuming Bowtie's executables
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1375 are under '/sw/bowtie/':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1376
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1377 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1378 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1379 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1380 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1381 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1382 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1383 --chipseq-target-read-files /data/mmliver_PolIIRep1.fq.gz,/data/mmliver_PolIIRep2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1384 --chipseq-control-read-files /data/mmliver_ChIPseqCtrl.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1385 --partition-model pk_lm2nopk \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1386 --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1387 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1388 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1389 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1390 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1391 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1392
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1393 9) Similar to the example in 8), suppose we want to derive prior from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1394 four histone modification ChIP-seq read data sets:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1395 '/data/H3K27Ac.fastq.gz', '/data/H3K4me1.fastq.gz',
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1396 '/data/H3K4me2.fastq.gz', and '/data/H3K4me3.fastq.gz'. Also, assuming
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1397 Bowtie's executables are under '/sw/bowtie/':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1398
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1399 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1400 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1401 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1402 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1403 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1404 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1405 --partition-model cmb_lgt \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1406 --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1407 --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1408 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1409 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1410 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1411 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1412 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1413
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1414 </help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1415 <citations>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1416 <citation type="doi">10.1186/1471-2105-12-323</citation>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1417 </citations>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1418
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419 artbio parents: diff changeset	1419 </tool>

Mercurial > repos > artbio > rsem

annotate rsem.xml @ 4:0fa0c1132a7b draft