salmon: salmon.xml annotate

annotate salmon.xml @ 8:8c23f01f10ae draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86

author	bgruening
date	Thu, 10 May 2018 06:48:12 -0400
parents	20007d82ae2d
children	32613ec39784

rev	line source
5 83bbe4e20bdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1b7f0370c3a5a8fd4ba2736607ad938a82a98b7b bgruening parents: 4 diff changeset	1 <tool id="salmon" name="Salmon" version="@VERSION@">
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	2
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	3 <description>Transcript Quantification from RNA-seq data</description>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	4
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	5 <macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	6 <xml name="strandedness">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	7 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	8 <option value="U" selected="True">Not stranded (U)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	11 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	12 </xml>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	13 <xml name="orientation">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	14 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	15 <option value="M">Mates are oriented in the same direction (M = matching)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	16 <option value="O">Mates are oriented away from each other (O = outward)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	17 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	18 </param>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	19 </xml>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	20 <token name="@VERSION@">0.9.1</token>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	21 </macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	22
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	23 <requirements>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	24 <requirement type="package" version="1.0.6">bzip2</requirement>
5 83bbe4e20bdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1b7f0370c3a5a8fd4ba2736607ad938a82a98b7b bgruening parents: 4 diff changeset	25 <requirement type="package" version="@VERSION@">salmon</requirement>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	26 <requirement type="package" version="1.2">seqtk</requirement>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	27 </requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	28
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	29 <stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	30 <exit_code range="1:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	31 <exit_code range=":-1" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	32 <regex match="Error:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	33 <regex match="Exception:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	34 <regex match="Exception :" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	35 </stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	36 <version_command>salmon -version</version_command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	37 <command><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	38 mkdir ./index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	39 &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	40 mkdir ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	41 #if $refTranscriptSource.TranscriptSource == "history":
3 0b689bf9473c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f bgruening parents: 0 diff changeset	42 &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	43 salmon index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	44 --transcripts $refTranscriptSource.ownFile
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	45 --kmerLen $refTranscriptSource.kmerLen
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	46 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	47 --index './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	48 --type '$quasi_orphans.type'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	49 $perfectHash
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	50 #if str($sasamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	51 --sasamp $sasamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	52 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	53 #set $index_path = './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	54 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	55 #set $index_path = $refTranscriptSource.index.fields.path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	56 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	57 &&
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	58 #set compressed = 'no'
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	59 #if $single_or_paired.single_or_paired_opts == 'single':
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	60 #if $single_or_paired.input_singles.ext == 'fasta':
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	61 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	62 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	63 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	64 #set compressed = 'GZ'
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	65 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	66 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	67 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	68 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	69 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	70 ln -s $single_or_paired.input_singles ./single.$ext &&
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	71 #else if $single_or_paired.single_or_paired_opts == 'paired':
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	72 #if $single_or_paired.input_mate1.ext == 'fasta':
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	73 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	74 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	75 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	76 #set compressed = 'GZ'
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	77 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	78 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	79 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	80 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	81 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	82 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	83 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	84 #else if $single_or_paired.single_or_paired_opts == 'paired_collection':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	85 #if $single_or_paired.input_1.forward.ext == 'fasta':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	86 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	87 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	88 #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	89 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	90 #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	91 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	92 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	93 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	94 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	95 ln -s ${single_or_paired.input_1.forward} ./mate1.$ext &&
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	96 ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext &&
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	97 #else if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	98 #if $single_or_paired.input_1.ext == 'fasta':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	99 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	100 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	101 #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	102 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	103 #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	104 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	105 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	106 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	107 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	108 ln -s $single_or_paired.input_1 ./mate1.$ext &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	109 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	110 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	111 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	112 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	113 salmon quant
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	114 --index $index_path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	115 #if $single_or_paired.single_or_paired_opts == 'single':
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	116 --libType ${single_or_paired.strandedness}
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	117 #if $compressed == 'GZ':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	118 --unmatedReads <(zcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	119 #else if $compressed == 'BZ2':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	120 --unmatedReads <(bzcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	121 #else:
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	122 --unmatedReads ./single.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	123 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	124 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	125 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	126 #if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	127 --mates1 <(bzcat < ./mate1.$ext \| seqtk seq -1)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	128 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	129 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	130 --mates1 <(seqtk seq -1 ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	131 --mates2 <(seqtk seq -2 ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	132 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	133 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	134 #if $compressed == 'GZ':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	135 --mates1 <(zcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	136 --mates2 <(zcat < ./mate2.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	137 #else if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	138 --mates1 <(bzcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	139 --mates2 <(bzcat < ./mate2.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	140 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	141 --mates1 ./mate1.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	142 --mates2 ./mate2.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	143 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	144 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	145 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	146 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	147 --output ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	148 #if str($quasi_orphans.type) == 'quasi':
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	149 --allowOrphans
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	150 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	151 $quasi_orphans.allowOrphans
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	152 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	153 $seqBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	154 $gcBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	155 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	156 --incompatPrior $adv.incompatPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	157 $adv.consistentHits
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	158 $adv.dumpEq
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	159 $adv.reduceGCMemory
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	160 #if str($adv.biasSpeedSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	161 --biasSpeedSamp $adv.biasSpeedSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	162 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	163 $adv.strictIntersect
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	164 #if str($adv.fldMax):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	165 --fldMax $adv.fldMax
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	166 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	167 #if str($adv.fldMean):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	168 --fldMean $adv.fldMean
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	169 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	170 #if str($adv.fldSD):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	171 --fldSD $adv.fldSD
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	172 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	173 #if $adv.forgettingFactor:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	174 --forgettingFactor $adv.forgettingFactor
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	175 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	176 #if str($adv.maxOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	177 --maxOcc $adv.maxOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	178 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	179 $adv.initUniform
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	180 $adv.noFragLengthDist
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	181 $adv.noBiasLengthThreshold
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	182 #if str($adv.maxReadOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	183 --maxReadOcc $adv.maxReadOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	184 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	185 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	186 --geneMap ./geneMap.${geneMap.ext}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	187 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	188 $adv.noEffectiveLengthCorrection
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	189 $adv.useVBOpt
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	190 #if str($adv.numBiasSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	191 --numBiasSamples $adv.numBiasSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	192 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	193 #if str($adv.numAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	194 --numAuxModelSamples $adv.numAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	195 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	196 #if str($adv.numPreAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	197 --numPreAuxModelSamples $adv.numPreAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	198 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	199 #if str($adv.numGibbsSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	200 --numGibbsSamples $adv.numGibbsSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	201 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	202 #if str($adv.numBootstraps):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	203 --numBootstraps $adv.numBootstraps
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	204 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	205 $adv.perTranscriptPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	206 #if $adv.vbPrior:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	207 --vbPrior $adv.vbPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	208 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	209 $adv.writeUnmappedNames
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	210 #if str($adv.writeMappings):
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	211 $adv.writeMappings > ${output_sam}
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	212 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	213 ]]>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	214 </command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	215
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	216 <inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	217 <conditional name="refTranscriptSource">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	218 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" help="Built-ins were indexed using default options">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	219 <option value="indexed">Use a built-in index</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	220 <option value="history" selected="True">Use one from the history</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	221 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	222 <when value="indexed">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	223 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	224 <options from_data_table="salmon_indexes">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	225 <filter type="sort_by" column="2"/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	226 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	227 </options>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	228 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	229 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	230 <when value="history">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	231 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	232 <param argument="kmerLen" type="integer" value="31" label="The size should be odd number."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	233 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	234 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	235 <conditional name="single_or_paired">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	236 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	237 <option value="single">Single-end</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	238 <option value="paired">Paired-end</option>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	239 <option value="paired_collection">Paired-end Dataset Collection</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	240 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	241 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	242 <when value="single">
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	243 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	244 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	245 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	246 <when value="paired">
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	247 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	248 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	249 <expand macro="orientation" />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	250 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	251 </when>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	252 <when value="paired_collection">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	253 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	254 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	255 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	256 </when>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	257 <when value="paired_interleaved">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	258 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	259 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	260 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	261 </when>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	262 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	263 <conditional name="quasi_orphans">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	264 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	265 <option value="quasi" selected="True">quasi</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	266 <option value="fmd">fmd</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	267 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	268 <when value="quasi">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	269 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	270 <when value="fmd">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	271 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	272 label="Consider orphaned reads as valid hits when performing lightweight-alignment"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	273 help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	274 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	275 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	276 <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	277 label="Perfect Hash"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	278 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct "/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	279 <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	280 help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	281 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	282 label="Perform sequence-specific bias correction"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	283 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	284 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	285 label="Perform fragment GC bias correction"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	286 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	287 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
6 aa4332ee7d1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7fae9d149b8b6aab2d01d94f137efc2967c7ee7 bgruening parents: 5 diff changeset	288 label="File containing a mapping of transcripts to genes"
aa4332ee7d1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7fae9d149b8b6aab2d01d94f137efc2967c7ee7 bgruening parents: 5 diff changeset	289 help="If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	290 <section name="adv" title="Additional Options">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	291 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	292 label="Write Mappings"
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	293 help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	294 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	295 label="Incompatible Prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	296 help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	297 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	298 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	299 <param argument="--reduceGCMemory" type="boolean" truevalue="--reduceGCMemory" falsevalue="" optional="True" checked="False"
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	300 label="If this option is selected, a more memory efficient (but slightly slower representation is used to compute fragment GC content."
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	301 help="Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same."/>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	302 <param argument="--biasSpeedSamp" type="integer" value="1" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	303 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	304 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	305 label="Modifies how orphans are assigned." help="When this flag is set, if the intersection of the quasi-mappings for the left and right is empty, then all mappings for the left and all mappings for the right read are reported as orphaned quasi-mappings."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	306 <param argument="--minLen" type="integer" value="19" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	307 label=" (S)MEMs smaller than this size won't be considered." help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	308 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	309 label="Perform sensitive quantification"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	310 help=" Setting this option enables the splitting of SMEMs that are larger than 1.5 times the minimum seed length (minLen/k above). This may reveal high scoring chains of MEMs that are masked by long SMEMs. However, this option makes lightweight-alignment a bit slower and is usually not necessary if the reference is of reasonable quality." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	311 <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	312 label="Force hits gathered during quasi-mapping to be consistent"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	313 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	314 <param argument="--extraSensitive" type="boolean" truevalue="--extraSensitive" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	315 label="Perform extra sensitive quantification"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	316 help="Setting this option enables an extra pass of 'seed' search. Enabling this option may improve sensitivity (the number of reads having sufficient coverage), but will typically slow down quantification by ~40%. Consider enabling this option if you find the mapping rate to be significantly lower than expected."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	317 <param argument="--coverage" type="float" value="0.69999999999999996" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	318 label="Required coverage of read by union of SMEMs to consider it a hit"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	319 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	320 <param argument="--fldMax" type="integer" value="1000" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	321 label="The maximum fragment length to consider when building the empirical distribution."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	322 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	323 <param argument="--fldMean" type="integer" value="200" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	324 label="The mean used in the fragment length distribution prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	325 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely mapping reads when performing paired-end quantification to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	326 <param argument="--fldSD" type="integer" value="80" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	327 label="Standard deviation"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	328 help="The standard deviation used in the fragment length distribution prior."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	329 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	330 label="The forgetting factor used in the online learning schedule."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	331 help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0]." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	332 <param argument="--maxOcc" type="integer" value="200" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	333 label="(S)MEMs occuring more than this many times won't be considered"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	334 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	335 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	336 label="Initialization with uniform parameters"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	337 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	338 <param argument="--maxReadOcc" type="integer" value="100" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	339 label="Maximal read mapping occurence"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	340 help="Reads mapping to more than this many places won't be considered."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	341 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	342 label="Disable effective length correction"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	343 help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	344 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	345 label="Ignore fragment length distribution"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	346 help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	347 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	348 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	349 help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	350 <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	351 label="Number of fragment mappings to use when learning the sequence-specific bias model."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	352 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	353 <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	354 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	355 help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	356 <param argument="--numPreAuxModelSamples" type="integer" value="1000000" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	357 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	358 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	359 <param argument="--splitWidth" type="integer" value="0" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	360 label=" If (S)MEM occurs fewer than this many times, search for smaller, contained MEMs"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	361 help="The default value will not split (S)MEMs, a higher value will result in more MEMs being explore and, thus, will result in increased running time." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	362 <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	363 label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	364 help="This can improve the fragment hit-rate, but is usually not necessary."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	365 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	366 label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	367 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	368 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	369 label=" Number of Gibbs sampling rounds to perform."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	370 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	371 <param argument="--numBootstraps" type="integer" value="0" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	372 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	373 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	374 <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	375 label="The prior will be interpreted as a transcript-level prior."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	376 help="either the default or the argument provided via --vbPrior" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	377 <param argument="--vbPrior" type="float" value="0.001" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	378 label="The prior that will be used in the VBEM algorithm."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	379 help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	380 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	381 label="Write the names of un-mapped reads to the file unmapped_names.txt."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	382 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	383 </section>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	384 </inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	385
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	386 <outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	387 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	388 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	389 <filter>geneMap</filter>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	390 </data>
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	391 <data name="output_sam" format="sam" label="${tool.name} on ${on_string} (SAM format)">
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	392 <filter>adv['writeMappings']</filter>
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	393 </data>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	394 </outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	395
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	396 <tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	397 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	398 <param name="single_or_paired_opts" value="paired" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	399 <param name="input_mate1" value="reads_1.fastq" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	400 <param name="input_mate2" value="reads_2.fastq" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	401 <param name="biasCorrect" value="False" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	402 <param name="TranscriptSource" value="history" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	403 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	404 <output name="output_quant">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	405 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	406 <has_text text="EffectiveLength" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	407 <has_text text="TPM" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	408 <has_text text="NM_001168316" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	409 <has_text text="NM_174914" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	410 <has_text text="NM_018953" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	411 <has_text text="NR_003084" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	412 <has_text text="NM_017410" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	413 <has_text text="NM_153693" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	414 <has_text text="NR_031764" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	415 <has_n_columns n="5" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	416 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	417 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	418 </test>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	419 <test> <!-- gzipped input -->
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	420 <param name="single_or_paired_opts" value="paired" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	421 <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	422 <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	423 <param name="biasCorrect" value="False" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	424 <param name="TranscriptSource" value="history" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	425 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	426 <output name="output_quant">
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	427 <assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	428 <has_text text="EffectiveLength" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	429 <has_text text="TPM" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	430 <has_text text="NM_001168316" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	431 <has_text text="NM_174914" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	432 <has_text text="NM_018953" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	433 <has_text text="NR_003084" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	434 <has_text text="NM_017410" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	435 <has_text text="NM_153693" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	436 <has_text text="NR_031764" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	437 <has_n_columns n="5" />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	438 </assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	439 </output>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	440 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	441 <test> <!-- bzipped input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	442 <param name="single_or_paired_opts" value="paired" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	443 <param name="input_mate1" value="reads_1.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	444 <param name="input_mate2" value="reads_2.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	445 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	446 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	447 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	448 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	449 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	450 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	451 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	452 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	453 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	454 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	455 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	456 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	457 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	458 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	459 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	460 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	461 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	462 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	463 <test> <!-- interleaved bz2 input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	464 <param name="single_or_paired_opts" value="paired_interleaved" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	465 <param name="input_1" value="reads_both.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	466 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	467 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	468 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	469 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	470 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	471 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	472 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	473 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	474 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	475 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	476 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	477 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	478 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	479 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	480 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	481 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	482 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	483 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	484 <test> <!-- interleaved gz input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	485 <param name="single_or_paired_opts" value="paired_interleaved" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	486 <param name="input_1" value="reads_both.fastq.gz" ftype="fastqsanger.gz" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	487 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	488 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	489 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	490 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	491 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	492 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	493 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	494 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	495 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	496 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	497 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	498 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	499 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	500 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	501 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	502 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	503 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	504 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	505 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	506 <param name="single_or_paired_opts" value="paired" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	507 <param name="input_mate1" value="reads_1.fastq" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	508 <param name="input_mate2" value="reads_2.fastq" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	509 <param name="TranscriptSource" value="history" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	510 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	511 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	512 <output name="output_quant">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	513 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	514 <has_text text="EffectiveLength" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	515 <has_text text="TPM" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	516 <has_text text="NM_001168316" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	517 <has_text text="NM_174914" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	518 <has_text text="NM_018953" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	519 <has_text text="NR_003084" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	520 <has_text text="NM_017410" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	521 <has_text text="NM_153693" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	522 <has_text text="NR_031764" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	523 <has_n_columns n="5" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	524 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	525 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	526 <output name="output_gene_quant">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	527 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	528 <has_text text="EffectiveLength" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	529 <has_text text="TPM" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	530 <has_text text="baz" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	531 <has_text text="bar" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	532 <has_text text="2283" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	533 <has_text text="1640" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	534 <has_n_columns n="5" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	535 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	536 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	537 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	538 <test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	539 <param name="single_or_paired_opts" value="paired_collection" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	540 <param name="input_1">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	541 <collection type="paired">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	542 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	543 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	544 </collection>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	545 </param>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	546 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	547 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	548 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	549 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	550 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	551 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	552 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	553 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	554 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	555 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	556 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	557 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	558 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	559 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	560 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	561 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	562 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	563 <output name="output_gene_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	564 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	565 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	566 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	567 <has_text text="baz" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	568 <has_text text="bar" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	569 <has_text text="2283" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	570 <has_text text="1640" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	571 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	572 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	573 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	574 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	575 </tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	576
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	577 <help><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	578 What it does
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	579 salmon is a tool for transcript quantification from RNA-seq data. It
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	580 requires a set of target transcripts (either from a reference or de-novo
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	581 assembly) to quantify. All you need to run Salmon is a fasta file containing
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	582 your reference transcripts and a (set of) fasta/fastq file(s) containing your
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	583 reads. Salmon runs in two phases; indexing and quantification. The indexing
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	584 step is independent of the reads, and only need to be run one for a particular
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	585 set of reference transcripts and choice of k (the k-mer size). The
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	586 quantification step, obviously, is specific to the set of RNA-seq reads and is
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	587 thus run more frequently.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	588 When the quantification output contains a number of columns:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	589 (1) Transcript ID,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	590 (2) Transcript Length,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	591 (3) Transcripts per Million (TPM) and
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	592 (4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	593 The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	594 The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	595 originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	596 (i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	597
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	598
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	599 Fragment Library Types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	600 ======================
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	601
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	602 There are numerous library preparation protocols for RNA-seq that result in
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	603 sequencing reads with different characteristics. For example, reads can be
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	604 single end (only one side of a fragment is recorded as a read) or paired-end
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	605 (reads are generated from both ends of a fragment). Further, the sequencing
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	606 reads themselves may be unstraned or strand-specific. Finally, paired-end
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	607 protocols will have a specified relative orientation. To characterize the
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	608 various different typs of sequencing libraries, we've created a miniature
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	609 "language" that allows for the succinct description of the many different types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	610 of possible fragment libraries. For paired-end reads, the possible
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	611 orientations, along with a graphical description of what they mean, are
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	612 illustrated below:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	613 .. image:: ReadLibraryIllustration.png
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	614 The library type string consists of three parts: the relative orientation of
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	615 the reads, the strandedness of the library, and the directionality of the
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	616 reads.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	617 The first part of the library string (relative orientation) is only provided if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	618 the library is paired-end. The possible options are:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	619 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	620
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	621 I = inward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	622 O = outward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	623 M = matching
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	624
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	625 The second part of the read library string specifies whether the protocol is
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	626 stranded or unstranded; the options are:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	627 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	628
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	629 S = stranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	630 U = unstranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	631
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	632 If the protocol is unstranded, then we're done. The final part of the library
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	633 string specifies the strand from which the read originates in a strand-specific
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	634 protocol — it is only provided if the library is stranded (i.e. if the
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	635 library format string is of the form S). The possible values are:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	636 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	637
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	638 F = read 1 (or single-end read) comes from the forward strand
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	639 R = read 1 (or single-end read) comes from the reverse strand
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	640
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	641 So, for example, if you wanted to specify a fragment library of strand-specific
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	642 paired-end reads, oriented toward each other, where read 1 comes from the
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	643 forward strand and read 2 comes from the reverse strand, you would specify ``-l
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	644 ISF`` on the command line. This designates that the library being processed has
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	645 the type "ISF" meaning, I\ nward (the relative orientation), S\ tranted
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	646 (the protocol is strand-specific), F\ orward (read 1 comes from the forward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	647 strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	648 The single end library strings are a bit simpler than their pair-end counter
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	649 parts, since there is no relative orientation of which to speak. Thus, the
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	650 only possible library format types for single-end reads are ``U`` (for
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	651 unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	652 and ``SR`` (for strand-specific reads coming from the reverse strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	653 A few more examples of some library format strings and their interpretations are:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	654 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	655
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	656 IU (an unstranded paired-end library where the reads face each other)
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	657
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	658 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	659
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	660 SF (a stranded single-end protocol where the reads come from the forward strand)
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	661
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	662 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	663
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	664 OSR (a stranded paired-end protocol where the reads face away from each other,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	665 read1 comes from reverse strand and read2 comes from the forward strand)
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	666
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	667 .. note:: Correspondence to TopHat library types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	668
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	669 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	670 read aligner has a different convention for specifying the format of the library.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	671 Below is a table that provides the corresponding Salmon/salmon library format
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	672 string for each of the potential TopHat library types:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	673
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	674 +---------------------+-------------------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	675 \| TopHat \| Salmon (and Sailfish) \|
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	676 +=====================+============+============+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	677 \| \| Paired-end \| Single-end \|
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	678 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	679 \|``-fr-unstranded`` \|``-l IU`` \|``-l U`` \|
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	680 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	681 \|``-fr-firststrand`` \|``-l ISR`` \|``-l SR`` \|
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	682 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	683 \|``-fr-secondstrand`` \|``-l ISF`` \|``-l SF`` \|
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	684 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	685
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	686 The remaining salmon library format strings are not directly expressible in terms
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	687 of the TopHat library types, and so there is no direct mapping for them.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	688 ]]> </help>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	689 <citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	690 <citation type="doi">10.1101/021592</citation>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	691 </citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	692 </tool>

Mercurial > repos > bgruening > salmon

annotate salmon.xml @ 8:8c23f01f10ae draft