salmon: salmon.xml annotate

annotate salmon.xml @ 6:aa4332ee7d1d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7fae9d149b8b6aab2d01d94f137efc2967c7ee7

author	bgruening
date	Fri, 30 Jun 2017 05:44:51 -0400
parents	83bbe4e20bdc
children	20007d82ae2d

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>
5 83bbe4e20bdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1b7f0370c3a5a8fd4ba2736607ad938a82a98b7b bgruening parents: 4 diff changeset	13 <token name="@VERSION@">0.8.2</token>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	14 </macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	15
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	16 <requirements>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	17 <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	18 <requirement type="package" version="@VERSION@">salmon</requirement>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	19 </requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	20
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	21 <stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	22 <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	23 <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	24 <regex match="Error:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	25 <regex match="Exception:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	26 <regex match="Exception :" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	27 </stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	28 <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	29 <command><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	30 mkdir ./index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	31 &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	32 mkdir ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	33 #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	34 &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	35 salmon index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	36 --transcripts $refTranscriptSource.ownFile
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	37 --kmerLen $refTranscriptSource.kmerLen
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	38 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	39 --index './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	40 --type '$quasi_orphans.type'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	41 $perfectHash
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	42 #if str($sasamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	43 --sasamp $sasamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	44 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	45 #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	46 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	47 #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	48 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	49 &&
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	50 #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	51 #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	52 #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	53 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	54 #else:
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	55 #if $single_or_paired.input_singles.is_of_type('fastq.gz'):
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	56 #set compressed = 'GZ'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	57 #else if $single_or_paired.input_singles.is_of_type('fastq.bz2'):
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	58 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	59 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	60 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	61 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	62 ln -s $single_or_paired.input_singles ./single.$ext &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	63 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	64 #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	65 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	66 #else:
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	67 #if $single_or_paired.input_mate1.is_of_type('fastq.gz'):
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	68 #set compressed = 'GZ'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	69 #else if $single_or_paired.input_mate1.is_of_type('fastq.bz2'):
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	70 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	71 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	72 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	73 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	74 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	75 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	76 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	77 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	78 ln -s "$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	79 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	80 salmon quant
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	81 --index $index_path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	82 #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	83 --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	84 #if $compressed == 'GZ':
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	85 --unmatedReads <(zcat ./single.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	86 #else if $compressed == 'BZ2':
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	87 --unmatedReads <(bzcat ./single.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	88 #else:
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	89 --unmatedReads ./single.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	90 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	91 #else:
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	92 #if $compressed == 'GZ':
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	93 --mates1 <(zcat ./mate1.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	94 --mates2 <(zcat ./mate2.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	95 #else if $compressed == 'BZ2':
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	96 --mates1 <(bzcat ./mate1.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	97 --mates2 <(bzcat ./mate2.$ext)
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	98 #else:
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	99 --mates1 ./mate1.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	100 --mates2 ./mate2.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	101 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	102 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	103 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	104 --output ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	105 #if str($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	106 --allowOrphans
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	107 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	108 $quasi_orphans.allowOrphans
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 $seqBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	111 $gcBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	112 --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	113 --incompatPrior $adv.incompatPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	114 $adv.consistentHits
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	115 $adv.dumpEq
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	116 #if str($adv.gcSizeSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	117 --gcSizeSamp $adv.gcSizeSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	118 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	119 #if str($adv.biasSpeedSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	120 --biasSpeedSamp $adv.biasSpeedSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	121 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	122 $adv.strictIntersect
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	123 #if str($adv.fldMax):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	124 --fldMax $adv.fldMax
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	125 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	126 #if str($adv.fldMean):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	127 --fldMean $adv.fldMean
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	128 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	129 #if str($adv.fldSD):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	130 --fldSD $adv.fldSD
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	131 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	132 #if $adv.forgettingFactor:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	133 --forgettingFactor $adv.forgettingFactor
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	134 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	135 $adv.writeMappings
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	136 #if str($adv.maxOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	137 --maxOcc $adv.maxOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	138 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	139 $adv.initUniform
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	140 $adv.noFragLengthDist
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	141 $adv.noBiasLengthThreshold
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	142 #if str($adv.maxReadOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	143 --maxReadOcc $adv.maxReadOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	144 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	145 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	146 --geneMap ./geneMap.${geneMap.ext}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	147 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	148 $adv.noEffectiveLengthCorrection
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	149 $adv.useVBOpt
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	150 #if str($adv.numBiasSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	151 --numBiasSamples $adv.numBiasSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	152 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	153 #if str($adv.numAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	154 --numAuxModelSamples $adv.numAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	155 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	156 #if str($adv.numPreAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	157 --numPreAuxModelSamples $adv.numPreAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	158 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	159 #if str($adv.numGibbsSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	160 --numGibbsSamples $adv.numGibbsSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	161 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	162 #if str($adv.numBootstraps):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	163 --numBootstraps $adv.numBootstraps
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	164 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	165 $adv.perTranscriptPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	166 #if $adv.vbPrior:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	167 --vbPrior $adv.vbPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	168 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	169 $adv.writeUnmappedNames
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	170 ]]>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	171 </command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	172
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	173 <inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	174 <conditional name="refTranscriptSource">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	175 <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	176 <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	177 <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	178 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	179 <when value="indexed">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	180 <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	181 <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	182 <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	183 <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	184 </options>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	185 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	186 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	187 <when value="history">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	188 <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	189 <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	190 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	191 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	192 <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	193 <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	194 <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	195 <option value="paired">Paired-end</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	196 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	197 <when value="single">
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	198 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" 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	199 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	200 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	201 <when value="paired">
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	202 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	203 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" 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	204 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	205 <option value="M">Mates are oriented in the same direction (M = matching)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	206 <option value="O">Mates are oriented away from each other (O = outward)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	207 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	208 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	209 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	210 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	211 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	212 <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	213 <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	214 <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	215 <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	216 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	217 <when value="quasi">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	218 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	219 <when value="fmd">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	220 <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	221 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	222 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	223 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	224 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	225 <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	226 label="Perfect Hash"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	227 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	228 <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	229 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	230 <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	231 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	232 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	233 <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	234 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	235 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	236 <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	237 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	238 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	239 <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	240 <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	241 label="Write Mappings"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	242 help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	243 <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	244 label="Incompatible Prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	245 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	246 <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	247 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	248 <param argument="--gcSizeSamp" 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	249 label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, 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	250 <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	251 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	252 <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	253 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	254 <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	255 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	256 <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	257 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	258 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	259 <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	260 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	261 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	262 <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	263 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	264 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	265 <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	266 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	267 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	268 <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	269 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	270 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	271 <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	272 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	273 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	274 <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	275 label="Standard deviation"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	276 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	277 <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	278 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	279 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	280 <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	281 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	282 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	283 <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	284 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	285 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	286 <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	287 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	288 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	289 <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	290 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	291 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	292 <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	293 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	294 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	295 <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	296 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	297 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	298 <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	299 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	300 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	301 <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	302 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	303 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	304 <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	305 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	306 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	307 <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	308 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	309 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	310 <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	311 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	312 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	313 <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	314 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	315 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	316 <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	317 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	318 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	319 <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	320 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	321 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	322 <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	323 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	324 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	325 <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	326 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	327 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	328 <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	329 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	330 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	331 </section>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	332 </inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	333
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	334 <outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	335 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	336 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${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	337 <filter>geneMap</filter>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	338 </data>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	339 </outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	340
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	341 <tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	342 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	362 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	363 </test>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	364 <test> <!-- gzipped input -->
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 </assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	384 </output>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	385 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	386 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	387 <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	388 <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	389 <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	390 <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	391 <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	392 <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	393 <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	394 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	395 <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	396 <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	397 <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	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	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 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	407 <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	408 <assert_contents>
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="EffectiveLength" />
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="TPM" />
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="baz" />
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="bar" />
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="2283" />
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="1640" />
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>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	419 </tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	420
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	421 <help><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	422 What it does
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	423 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	424 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	425 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	426 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	427 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	428 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	429 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	430 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	431 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	432 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	433 (1) Transcript ID,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	434 (2) Transcript Length,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	435 (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	436 (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	437 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	438 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	439 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	440 (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	441
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	442
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	443 Fragment Library Types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	444 ======================
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	445
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	446 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	447 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	448 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	449 (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	450 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	451 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	452 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	453 "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	454 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	455 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	456 illustrated below:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	457 .. image:: ReadLibraryIllustration.png
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	458 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	459 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	460 reads.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	461 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	462 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	463 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	464
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	465 I = inward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	466 O = outward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	467 M = matching
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	468
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	469 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	470 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	471 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	472
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	473 S = stranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	474 U = unstranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	475
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	476 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	477 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	478 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	479 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	480 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	481
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	482 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	483 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	484
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	485 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	486 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	487 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	488 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	489 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	490 (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	491 strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	492 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	493 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	494 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	495 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	496 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	497 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	498 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	499
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	500 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	501
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	502 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	503
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	504 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	505
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	506 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	507
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	508 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	509 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	510
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	511 .. 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	512
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	513 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	514 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	515 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	516 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	517
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	518 +---------------------+-------------------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	519 \| 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	520 +=====================+============+============+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	521 \| \| 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	522 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	523 \|``-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	524 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	525 \|``-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	526 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	527 \|``-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	528 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	529
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	530 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	531 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	532 ]]> </help>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	533 <citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	534 <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	535 </citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	536 </tool>

Mercurial > repos > bgruening > salmon

annotate salmon.xml @ 6:aa4332ee7d1d draft