salmon: salmon.xml annotate

annotate salmon.xml @ 10:d9bfffca4548 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56

author	bgruening
date	Thu, 23 Aug 2018 15:58:10 -0400
parents	32613ec39784
children	c320b539ff54

rev	line source
5 83bbe4e20bdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1b7f0370c3a5a8fd4ba2736607ad938a82a98b7b bgruening parents: 4 diff changeset	1 <tool id="salmon" name="Salmon" version="@VERSION@">
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	2
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	3 <description>Transcript Quantification from RNA-seq data</description>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	4
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	5 <macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	6 <xml name="strandedness">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	7 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	8 <option value="U" selected="True">Not stranded (U)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	11 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	12 </xml>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	13 <xml name="orientation">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	14 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	15 <option value="M">Mates are oriented in the same direction (M = matching)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	16 <option value="O">Mates are oriented away from each other (O = outward)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	17 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	18 </param>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	19 </xml>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	20 <token name="@VERSION@">0.11.2</token>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	21 </macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	22
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	23 <requirements>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	24 <requirement type="package" version="1.0.6">bzip2</requirement>
5 83bbe4e20bdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1b7f0370c3a5a8fd4ba2736607ad938a82a98b7b bgruening parents: 4 diff changeset	25 <requirement type="package" version="@VERSION@">salmon</requirement>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	26 <requirement type="package" version="1.2">seqtk</requirement>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	27 </requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	28
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	29 <stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	30 <exit_code range="1:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	31 <exit_code range=":-1" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	32 <regex match="Error:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	33 <regex match="Exception:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	34 <regex match="Exception :" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	35 </stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	36 <version_command>salmon -version</version_command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	37 <command><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	38 mkdir ./index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	39 &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	40 mkdir ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	41 #if $refTranscriptSource.TranscriptSource == "history":
3 0b689bf9473c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f bgruening parents: 0 diff changeset	42 &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	43 salmon index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	44 --transcripts $refTranscriptSource.ownFile
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	45 --kmerLen $refTranscriptSource.kmerLen
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	46 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	47 --index './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	48 --type '$quasi_orphans.type'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	49 $perfectHash
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	50 #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	51 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	52 #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	53 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	54 &&
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	55 #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	56 #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	57 #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	58 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	59 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	60 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	61 #set compressed = 'GZ'
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	62 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	63 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	64 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	65 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	66 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	67 ln -s $single_or_paired.input_singles ./single.$ext &&
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	68 #else if $single_or_paired.single_or_paired_opts == 'paired':
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	69 #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	70 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	71 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	72 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	73 #set compressed = 'GZ'
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	74 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	75 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	76 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	77 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	78 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	79 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	80 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	81 #else if $single_or_paired.single_or_paired_opts == 'paired_collection':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	82 #if $single_or_paired.input_1.forward.ext == 'fasta':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	83 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	84 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	85 #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	86 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	87 #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	88 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	89 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	90 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	91 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	92 ln -s ${single_or_paired.input_1.forward} ./mate1.$ext &&
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	93 ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext &&
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	94 #else if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	95 #if $single_or_paired.input_1.ext == 'fasta':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	96 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	97 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	98 #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	99 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	100 #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	101 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	102 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	103 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	104 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	105 ln -s $single_or_paired.input_1 ./mate1.$ext &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	106 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	107 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	108 ln -s "$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	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 salmon quant
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	111 --index $index_path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	112 #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	113 --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	114 #if $compressed == 'GZ':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	115 --unmatedReads <(zcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	116 #else if $compressed == 'BZ2':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	117 --unmatedReads <(bzcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	118 #else:
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	119 --unmatedReads ./single.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	120 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	121 #else:
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	122 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	123 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	124 #if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	125 --mates1 <(bzcat < ./mate1.$ext \| seqtk seq -1)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	126 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	127 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	128 --mates1 <(seqtk seq -1 ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	129 --mates2 <(seqtk seq -2 ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	130 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	131 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	132 #if $compressed == 'GZ':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	133 --mates1 <(zcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	134 --mates2 <(zcat < ./mate2.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	135 #else if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	136 --mates1 <(bzcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	137 --mates2 <(bzcat < ./mate2.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	138 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	139 --mates1 ./mate1.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	140 --mates2 ./mate2.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	141 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	142 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	143 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	144 --output ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	145 #if str($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	146 --allowOrphans
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	147 $quasi_orphans.validateMappings
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	148 --ma $quasi_orphans.matchScore
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	149 --mp $quasi_orphans.mismatchPenalty
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	150 --go $quasi_orphans.gapOpenPenalty
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	151 --ge $quasi_orphans.gapExtensionPenalty
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	152 --minScoreFraction $quasi_orphans.minScoreFraction
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	153 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	154 $seqBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	155 $gcBias
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	156 $noErrorModel
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	157 --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	158 --incompatPrior $adv.incompatPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	159 $adv.consistentHits
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	160 $adv.dumpEq
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	161 $adv.reduceGCMemory
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	162 #if str($adv.biasSpeedSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	163 --biasSpeedSamp $adv.biasSpeedSamp
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 $adv.strictIntersect
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	166 #if str($adv.fldMax):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	167 --fldMax $adv.fldMax
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	168 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	169 #if str($adv.fldMean):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	170 --fldMean $adv.fldMean
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	171 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	172 #if str($adv.fldSD):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	173 --fldSD $adv.fldSD
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	174 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	175 #if $adv.forgettingFactor:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	176 --forgettingFactor $adv.forgettingFactor
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	177 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	178 $adv.initUniform
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	179 $adv.noFragLengthDist
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	180 $adv.noBiasLengthThreshold
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	181 #if str($adv.maxReadOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	182 --maxReadOcc $adv.maxReadOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	183 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	184 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	185 --geneMap ./geneMap.${geneMap.ext}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	186 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	187 $adv.noEffectiveLengthCorrection
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	188 $adv.useEM
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	189 #if str($adv.numBiasSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	190 --numBiasSamples $adv.numBiasSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	191 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	192 #if str($adv.numAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	193 --numAuxModelSamples $adv.numAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	194 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	195 #if str($adv.numPreAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	196 --numPreAuxModelSamples $adv.numPreAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	197 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	198 #if str($adv.numGibbsSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	199 --numGibbsSamples $adv.numGibbsSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	200 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	201 #if str($adv.numBootstraps):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	202 --numBootstraps $adv.numBootstraps
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	203 #end if
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	204 #if str($adv.consensusSlack):
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	205 --consensusSlack $adv.consensusSlack
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	206 #else:
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	207 #if $quasi_orphans.validateMappings:
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	208 --consensusSlack 1
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	209 #else:
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	210 --consensusSlack 0
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	211 #end if
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	212 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	213 $adv.perTranscriptPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	214 #if $adv.vbPrior:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	215 --vbPrior $adv.vbPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	216 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	217 $adv.writeUnmappedNames
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	218 --sigDigits $adv.sigDigits
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	219 #if str($adv.writeMappings):
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	220 $adv.writeMappings > ${output_sam}
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	221 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	222 ]]>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	223 </command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	224
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	225 <inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	226 <conditional name="refTranscriptSource">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	227 <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	228 <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	229 <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	230 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	231 <when value="indexed">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	232 <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	233 <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	234 <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	235 <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	236 </options>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	237 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	238 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	239 <when value="history">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	240 <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	241 <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	242 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	243 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	244 <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	245 <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	246 <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	247 <option value="paired">Paired-end</option>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	248 <option value="paired_collection">Paired-end Dataset Collection</option>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	249 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	250 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	251 <when value="single">
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	252 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	253 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	254 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	255 <when value="paired">
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	256 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	257 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	258 <expand macro="orientation" />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	259 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	260 </when>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	261 <when value="paired_collection">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	262 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	263 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	264 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	265 </when>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	266 <when value="paired_interleaved">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	267 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	268 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	269 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	270 </when>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	271 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	272 <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	273 <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	274 <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	275 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	276 <when value="quasi">
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	277 <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	278 label="Validate mappings"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	279 help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	280 <param name="matchScore" argument="--ma" type="integer" value="2"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	281 label="Match Score"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	282 help="The value given to a match between read and reference nucleotides in an alignment."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	283 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	284 label="Mismatch Penalty"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	285 help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	286 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	287 label="Gap Open Penalty"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	288 help="The value given to a gap opening in an alignment."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	289 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	290 label="Gap Extension Penalty"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	291 help="The value given to a gap extension in an alignment."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	292 <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	293 label="Min Score Fraction"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	294 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	295 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	296 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	297 <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	298 label="Perfect Hash"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	299 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	300 <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	301 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	302 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	303 <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	304 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	305 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	306 <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	307 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	308 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." />
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	309 <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	310 label="No Error Model"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	311 help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	312 <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	313 <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	314 label="Write Mappings"
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	315 help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	316 <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	317 label="Incompatible Prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	318 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	319 <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	320 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	321 <param argument="--reduceGCMemory" type="boolean" truevalue="--reduceGCMemory" falsevalue="" optional="True" checked="False"
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	322 label="If this option is selected, a more memory efficient (but slightly slower representation is used to compute fragment GC content."
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	323 help="Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same."/>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	324 <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	325 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	326 <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	327 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	328 <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	329 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	330 <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	331 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	332 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	333 <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	334 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	335 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	336 <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	337 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	338 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	339 <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	340 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	341 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	342 <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	343 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	344 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	345 <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	346 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	347 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	348 <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	349 label="Standard deviation"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	350 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	351 <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	352 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	353 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	354 <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	355 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	356 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	357 <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	358 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	359 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	360 <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	361 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	362 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	363 <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	364 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	365 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	366 <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	367 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	368 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	369 <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	370 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	371 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	372 <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	373 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	374 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	375 <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	376 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	377 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	378 <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	379 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	380 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	381 <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	382 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	383 help="This can improve the fragment hit-rate, but is usually not necessary."/>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	384 <param argument="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	385 label="Use the traditional EM algorithm for optimization in the batch passes."
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	386 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	387 <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	388 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	389 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	390 <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	391 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	392 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	393 <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	394 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	395 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	396 <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	397 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	398 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	399 <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	400 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	401 help=""/>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	402 <param argument="--sigDigits" type="integer" value="3"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	403 label="Significant Digits"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	404 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	405 <param argument="--consensusSlack" type="integer" optional="True"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	406 label="Consensus Slack"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	407 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	408 </section>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	409 </inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	410
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	411 <outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	412 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	413 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	414 <filter>geneMap</filter>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	415 </data>
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	416 <data name="output_sam" format="sam" label="${tool.name} on ${on_string} (SAM format)">
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	417 <filter>adv['writeMappings']</filter>
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	418 </data>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	419 </outputs>
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 <tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	422 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	423 <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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	431 <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	432 <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	433 <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	434 <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	435 <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	436 <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	437 <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	438 <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	439 <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	440 <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	441 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	442 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	443 </test>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	444 <test> <!-- gzipped input -->
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	445 <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	446 <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	447 <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	448 <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	449 <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	450 <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	451 <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	452 <assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	453 <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	454 <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	455 <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	456 <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	457 <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	458 <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	459 <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	460 <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	461 <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	462 <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	463 </assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	464 </output>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	465 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	466 <test> <!-- bzipped input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	467 <param name="single_or_paired_opts" value="paired" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	468 <param name="input_mate1" value="reads_1.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	469 <param name="input_mate2" value="reads_2.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	470 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	471 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	472 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	473 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	474 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	475 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	476 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	477 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	478 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	479 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	480 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	481 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	482 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	483 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	484 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	485 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	486 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	487 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	488 <test> <!-- interleaved bz2 input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	489 <param name="single_or_paired_opts" value="paired_interleaved" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	490 <param name="input_1" value="reads_both.fastq.bz2" ftype="fastqsanger.bz2" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	491 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	492 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	493 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	494 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	495 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	496 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	497 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	498 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	499 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	500 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	501 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	502 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	503 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	504 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	505 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	506 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	507 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	508 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	509 <test> <!-- interleaved gz input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	510 <param name="single_or_paired_opts" value="paired_interleaved" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	511 <param name="input_1" value="reads_both.fastq.gz" ftype="fastqsanger.gz" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	512 <param name="biasCorrect" value="False" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	513 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	514 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	515 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	516 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	517 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	518 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	519 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	520 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	521 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	522 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	523 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	524 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	525 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	526 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	527 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	528 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	529 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	530 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	531 <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	532 <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	533 <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	534 <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	535 <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	536 <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	537 <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	538 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	539 <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	540 <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	541 <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	542 <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	543 <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	544 <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	545 <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	546 <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	547 <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	548 <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	549 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	550 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	551 <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	552 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	553 <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	554 <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	555 <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	556 <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	557 <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	558 <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	559 <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	560 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	561 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	562 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	563 <test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	564 <param name="single_or_paired_opts" value="paired_collection" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	565 <param name="input_1">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	566 <collection type="paired">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	567 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	568 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	569 </collection>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	570 </param>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	571 <param name="TranscriptSource" value="history" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	572 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	573 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	574 <output name="output_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	575 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	576 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	577 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	578 <has_text text="NM_001168316" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	579 <has_text text="NM_174914" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	580 <has_text text="NM_018953" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	581 <has_text text="NR_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	582 <has_text text="NM_017410" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	583 <has_text text="NM_153693" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	584 <has_text text="NR_031764" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	585 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	586 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	587 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	588 <output name="output_gene_quant">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	589 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	590 <has_text text="EffectiveLength" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	591 <has_text text="TPM" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	592 <has_text text="baz" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	593 <has_text text="bar" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	594 <has_text text="2283" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	595 <has_text text="1640" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	596 <has_n_columns n="5" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	597 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	598 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	599 </test>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	600 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	601 <param name="single_or_paired_opts" value="paired" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	602 <param name="input_mate1" value="reads_1.fastq" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	603 <param name="input_mate2" value="reads_2.fastq" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	604 <param name="TranscriptSource" value="history" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	605 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	606 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	607 <param name="validateMappings" value="True" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	608 <output name="output_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	609 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	610 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	611 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	612 <has_text text="NM_001168316" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	613 <has_text text="NM_174914" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	614 <has_text text="NM_018953" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	615 <has_text text="NR_003084" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	616 <has_text text="NM_017410" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	617 <has_text text="NM_153693" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	618 <has_text text="NR_031764" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	619 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	620 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	621 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	622 <output name="output_gene_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	623 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	624 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	625 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	626 <has_text text="baz" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	627 <has_text text="bar" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	628 <has_text text="2283" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	629 <has_text text="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	630 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	631 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	632 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	633 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	634 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	635 <param name="single_or_paired_opts" value="paired_collection" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	636 <param name="input_1">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	637 <collection type="paired">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	638 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	639 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	640 </collection>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	641 </param>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	642 <param name="TranscriptSource" value="history" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	643 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	644 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	645 <param name="validateMappings" value="True" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	646 <output name="output_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	647 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	648 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	649 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	650 <has_text text="NM_001168316" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	651 <has_text text="NM_174914" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	652 <has_text text="NM_018953" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	653 <has_text text="NR_003084" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	654 <has_text text="NM_017410" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	655 <has_text text="NM_153693" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	656 <has_text text="NR_031764" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	657 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	658 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	659 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	660 <output name="output_gene_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	661 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	662 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	663 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	664 <has_text text="baz" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	665 <has_text text="bar" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	666 <has_text text="2283" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	667 <has_text text="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	668 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	669 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	670 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	671 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	672 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	673 <param name="single_or_paired_opts" value="paired" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	674 <param name="input_mate1" value="reads_1.fastq" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	675 <param name="input_mate2" value="reads_2.fastq" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	676 <param name="TranscriptSource" value="history" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	677 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	678 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	679 <param name="useEM" value="True" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	680 <output name="output_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	681 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	682 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	683 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	684 <has_text text="NM_001168316" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	685 <has_text text="NM_174914" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	686 <has_text text="NM_018953" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	687 <has_text text="NR_003084" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	688 <has_text text="NM_017410" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	689 <has_text text="NM_153693" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	690 <has_text text="NR_031764" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	691 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	692 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	693 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	694 <output name="output_gene_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	695 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	696 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	697 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	698 <has_text text="baz" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	699 <has_text text="bar" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	700 <has_text text="2283" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	701 <has_text text="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	702 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	703 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	704 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	705 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	706 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	707 <param name="single_or_paired_opts" value="paired_collection" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	708 <param name="input_1">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	709 <collection type="paired">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	710 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	711 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	712 </collection>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	713 </param>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	714 <param name="TranscriptSource" value="history" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	715 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	716 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	717 <param name="useEM" value="True" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	718 <output name="output_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	719 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	720 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	721 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	722 <has_text text="NM_001168316" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	723 <has_text text="NM_174914" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	724 <has_text text="NM_018953" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	725 <has_text text="NR_003084" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	726 <has_text text="NM_017410" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	727 <has_text text="NM_153693" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	728 <has_text text="NR_031764" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	729 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	730 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	731 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	732 <output name="output_gene_quant">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	733 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	734 <has_text text="EffectiveLength" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	735 <has_text text="TPM" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	736 <has_text text="baz" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	737 <has_text text="bar" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	738 <has_text text="2283" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	739 <has_text text="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	740 <has_n_columns n="5" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	741 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	742 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	743 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	744 </tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	745
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	746 <help><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	747 What it does
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	748 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	749 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	750 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	751 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	752 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	753 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	754 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	755 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	756 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	757 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	758 (1) Transcript ID,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	759 (2) Transcript Length,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	760 (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	761 (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	762 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	763 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	764 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	765 (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	766
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	767
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	768 Fragment Library Types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	769 ======================
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	770
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	771 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	772 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	773 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	774 (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	775 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	776 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	777 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	778 "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	779 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	780 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	781 illustrated below:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	782 .. image:: ReadLibraryIllustration.png
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	783 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	784 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	785 reads.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	786 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	787 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	788 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	789
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	790 I = inward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	791 O = outward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	792 M = matching
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	793
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	794 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	795 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	796 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	797
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	798 S = stranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	799 U = unstranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	800
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	801 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	802 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	803 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	804 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	805 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	806
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	807 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	808 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	809
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	810 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	811 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	812 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	813 ISF`` on the command line. This designates that the library being processed has
9 32613ec39784 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit bae8cc7d7a88154b815acc3cd126010e7e965d5c bgruening parents: 8 diff changeset	814 the type "ISF" meaning, I\ nward (the relative orientation), S\ tranded
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	815 (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	816 strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	817 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	818 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	819 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	820 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	821 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	822 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	823 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	824
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	825 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	826
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	827 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	828
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	829 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	830
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	831 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	832
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	833 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	834 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	835
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	836 .. 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	837
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	838 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	839 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	840 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	841 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	842
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	843 +---------------------+-------------------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	844 \| 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	845 +=====================+============+============+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	846 \| \| 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	847 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	848 \|``-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	849 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	850 \|``-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	851 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	852 \|``-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	853 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	854
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	855 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	856 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	857 ]]> </help>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	858 <citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	859 <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	860 </citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	861 </tool>

Mercurial > repos > bgruening > salmon

annotate salmon.xml @ 10:d9bfffca4548 draft