salmon: salmon.xml annotate

annotate salmon.xml @ 11:c320b539ff54 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72

author	bgruening
date	Thu, 25 Jul 2019 15:45:02 -0400
parents	d9bfffca4548
children

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>
11 c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	21 <token name="@IDX_VERSION@">q5</token>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	22 </macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	23
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	24 <requirements>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	25 <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	26 <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	27 <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	28 </requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	29
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	30 <stdio>
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 <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	33 <regex match="Error:" />
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 <regex match="Exception :" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	36 </stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	37 <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	38 <command><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	39 mkdir ./index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	40 &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	41 mkdir ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	42 #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	43 &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	44 salmon index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	45 --transcripts $refTranscriptSource.ownFile
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	46 --kmerLen $refTranscriptSource.kmerLen
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	47 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	48 --index './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	49 --type '$quasi_orphans.type'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	50 $perfectHash
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	51 #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	52 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	53 #set $index_path = $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	54 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	55 &&
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	56 #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	57 #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	58 #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	59 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	60 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	61 #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	62 #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	63 #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	64 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	65 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	66 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	67 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	68 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	69 #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	70 #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	71 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	72 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	73 #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	74 #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	75 #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	76 #set compressed = 'BZ2'
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	77 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	78 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	79 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	80 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	81 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	82 #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	83 #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	84 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	85 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	86 #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	87 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	88 #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	89 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	90 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	91 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	92 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	93 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	94 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	95 #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	96 #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	97 #set $ext = 'fasta'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	98 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	99 #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	100 #set compressed = 'GZ'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	101 #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	102 #set compressed = 'BZ2'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	103 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	104 #set $ext = 'fastq'
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	105 #end if
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	106 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	107 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	108 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	109 ln -s "$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	110 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	111 salmon quant
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	112 --index $index_path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	113 #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	114 --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	115 #if $compressed == 'GZ':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	116 --unmatedReads <(zcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	117 #else if $compressed == 'BZ2':
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	118 --unmatedReads <(bzcat < ./single.$ext)
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	119 #else:
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	120 --unmatedReads ./single.$ext
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	121 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	122 #else:
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	123 --libType "${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	124 #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	125 #if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	126 --mates1 <(bzcat < ./mate1.$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	127 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	128 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	129 --mates1 <(seqtk seq -1 ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	130 --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	131 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	132 #else:
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	133 #if $compressed == 'GZ':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	134 --mates1 <(zcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	135 --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	136 #else if $compressed == 'BZ2':
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	137 --mates1 <(bzcat < ./mate1.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	138 --mates2 <(bzcat < ./mate2.$ext)
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	139 #else:
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	140 --mates1 ./mate1.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	141 --mates2 ./mate2.$ext
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	142 #end if
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	143 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	144 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	145 --output ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	146 #if str($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	147 --allowOrphans
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	148 $quasi_orphans.validateMappings
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	149 --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	150 --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	151 --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	152 --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	153 --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	154 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	155 $seqBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	156 $gcBias
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	157 $noErrorModel
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	158 --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	159 --incompatPrior $adv.incompatPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	160 $adv.consistentHits
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	161 $adv.dumpEq
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	162 $adv.reduceGCMemory
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	163 #if str($adv.biasSpeedSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	164 --biasSpeedSamp $adv.biasSpeedSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	165 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	166 $adv.strictIntersect
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	167 #if str($adv.fldMax):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	168 --fldMax $adv.fldMax
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	169 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	170 #if str($adv.fldMean):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	171 --fldMean $adv.fldMean
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	172 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	173 #if str($adv.fldSD):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	174 --fldSD $adv.fldSD
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	175 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	176 #if $adv.forgettingFactor:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	177 --forgettingFactor $adv.forgettingFactor
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	178 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	179 $adv.initUniform
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	180 $adv.noFragLengthDist
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	181 $adv.noBiasLengthThreshold
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	182 #if str($adv.maxReadOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	183 --maxReadOcc $adv.maxReadOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	184 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	185 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	186 --geneMap ./geneMap.${geneMap.ext}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	187 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	188 $adv.noEffectiveLengthCorrection
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	189 $adv.useEM
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	190 #if str($adv.numBiasSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	191 --numBiasSamples $adv.numBiasSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	192 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	193 #if str($adv.numAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	194 --numAuxModelSamples $adv.numAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	195 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	196 #if str($adv.numPreAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	197 --numPreAuxModelSamples $adv.numPreAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	198 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	199 #if str($adv.numGibbsSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	200 --numGibbsSamples $adv.numGibbsSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	201 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	202 #if str($adv.numBootstraps):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	203 --numBootstraps $adv.numBootstraps
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	204 #end if
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	205 #if str($adv.consensusSlack):
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	206 --consensusSlack $adv.consensusSlack
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	207 #else:
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	208 #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	209 --consensusSlack 1
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	210 #else:
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	211 --consensusSlack 0
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	212 #end if
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	213 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	214 $adv.perTranscriptPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	215 #if $adv.vbPrior:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	216 --vbPrior $adv.vbPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	217 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	218 $adv.writeUnmappedNames
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	219 --sigDigits $adv.sigDigits
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	220 #if str($adv.writeMappings):
20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	221 $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	222 #end if
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	223 ]]>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	224 </command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	225
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	226 <inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	227 <conditional name="refTranscriptSource">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	228 <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	229 <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	230 <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	231 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	232 <when value="indexed">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	233 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
11 c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	234 <options from_data_table="salmon_indexes_versioned">
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	235 <filter type="sort_by" column="2"/>
11 c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	236 <filter type="static_value" column="4" value="@IDX_VERSION@" />
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	237 <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	238 </options>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	239 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	240 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	241 <when value="history">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	242 <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	243 <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	244 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	245 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	253 <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	254 <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	255 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	256 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	257 <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	258 <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	259 <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	260 <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	261 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	262 </when>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	263 <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	264 <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	265 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	266 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	267 </when>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	268 <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	269 <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	270 <expand macro="orientation" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	271 <expand macro="strandedness" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	272 </when>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	273 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	274 <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	275 <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	276 <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	277 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	278 <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	279 <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	280 label="Validate mappings"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	281 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	282 <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	283 label="Match Score"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	284 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	285 <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	286 label="Mismatch Penalty"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	287 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	288 <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	289 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	290 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	291 <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	292 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	293 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	294 <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	295 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	296 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	297 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	298 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	299 <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	300 label="Perfect Hash"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	301 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	302 <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	303 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	304 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	305 <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	306 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	307 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	308 <param argument="--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	309 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	310 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	311 <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	312 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	313 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	314 <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	315 <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	316 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	317 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	318 <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	319 label="Incompatible Prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	320 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	321 <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	322 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	323 <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	324 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	325 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	326 <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	327 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	328 <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	329 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	330 <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	331 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	332 <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	333 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	334 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	335 <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	336 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	337 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	338 <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	339 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	340 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	341 <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	342 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	343 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	344 <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	345 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	346 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	347 <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	348 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	349 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	350 <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	351 label="Standard deviation"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	352 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	353 <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	354 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	355 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	356 <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	357 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	358 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	359 <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	360 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	361 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	362 <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	363 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	364 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	365 <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	366 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	367 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	368 <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	369 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	370 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	371 <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	372 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	373 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	374 <param argument="--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	375 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	376 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	377 <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	378 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	379 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	380 <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	381 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	382 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	383 <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	384 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	385 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	386 <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	387 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	388 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	389 <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	390 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	391 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	392 <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	393 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	394 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	395 <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	396 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	397 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	398 <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	399 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	400 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	401 <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	402 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	403 help=""/>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	404 <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	405 label="Significant Digits"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	406 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	407 <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	408 label="Consensus Slack"
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	409 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	410 </section>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	411 </inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	412
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	413 <outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	414 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	415 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	416 <filter>geneMap</filter>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	417 </data>
7 20007d82ae2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa bgruening parents: 6 diff changeset	418 <data name="output_sam" format="sam" label="${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	419 <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	420 </data>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	421 </outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	422
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	423 <tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	424 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	425 <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	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 <assert_contents>
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="EffectiveLength" />
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="TPM" />
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_001168316" />
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="NM_174914" />
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_018953" />
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="NR_003084" />
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="NM_017410" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	440 <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	441 <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	442 <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	443 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	444 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	445 </test>
11 c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	446 <test> <!--test use of built-in index-->
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	447 <param name="single_or_paired_opts" value="paired" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	448 <param name="input_mate1" value="reads_1.fastq" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	449 <param name="input_mate2" value="reads_2.fastq" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	450 <param name="biasCorrect" value="False" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	451 <param name="TranscriptSource" value="indexed" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	452 <param name="index" value="hg19_transcript_subset" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	453 <output name="output_quant">
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	454 <assert_contents>
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	455 <has_text text="EffectiveLength" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	456 <has_text text="TPM" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	457 <has_text text="NM_001168316" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	458 <has_text text="NM_174914" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	459 <has_text text="NM_018953" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	460 <has_text text="NR_003084" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	461 <has_text text="NM_017410" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	462 <has_text text="NM_153693" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	463 <has_text text="NR_031764" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	464 <has_n_columns n="5" />
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	465 </assert_contents>
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	466 </output>
c320b539ff54 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72 bgruening parents: 10 diff changeset	467 </test>
4 979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	468 <test> <!-- gzipped input -->
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	469 <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	470 <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	471 <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	472 <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	473 <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	474 <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	475 <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	476 <assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	477 <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	478 <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	479 <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	480 <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	481 <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	482 <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	483 <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	484 <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	485 <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	486 <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	487 </assert_contents>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	488 </output>
979bff04ae7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243 bgruening parents: 3 diff changeset	489 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	490 <test> <!-- bzipped input -->
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	491 <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	492 <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	493 <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	494 <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	495 <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	496 <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	497 <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	498 <assert_contents>
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="EffectiveLength" />
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="TPM" />
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="NM_001168316" />
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_174914" />
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_018953" />
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_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	505 <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	506 <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	507 <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	508 <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	509 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	510 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	511 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	512 <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	513 <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	514 <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	515 <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	516 <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	517 <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	518 <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	519 <assert_contents>
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="EffectiveLength" />
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="TPM" />
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="NM_001168316" />
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_174914" />
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_018953" />
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_003084" />
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	526 <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	527 <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	528 <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	529 <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	530 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	531 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	532 </test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	533 <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	534 <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	535 <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	536 <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	537 <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	538 <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	539 <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	540 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	541 <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	542 <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	543 <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	544 <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	545 <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	546 <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	547 <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	548 <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	549 <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	550 <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	551 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	552 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	553 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	554 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	555 <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	556 <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	557 <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	558 <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	559 <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	560 <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	561 <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	562 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	563 <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	564 <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	565 <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	566 <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	567 <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	568 <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	569 <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	570 <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	571 <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	572 <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	573 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	574 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	575 <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	576 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	577 <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	578 <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	579 <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	580 <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	581 <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	582 <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	583 <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	584 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	585 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	586 </test>
8 8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	587 <test>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	588 <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	589 <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	590 <collection type="paired">
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	591 <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	592 <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	593 </collection>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	594 </param>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	595 <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	596 <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	597 <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	598 <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	599 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	600 <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	601 <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	602 <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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 <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	610 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	611 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	612 <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	613 <assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	614 <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	615 <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	616 <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	617 <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	618 <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	619 <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	620 <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	621 </assert_contents>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	622 </output>
8c23f01f10ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 bgruening parents: 7 diff changeset	623 </test>
10 d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	624 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	625 <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	626 <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	627 <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	628 <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	629 <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	630 <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	631 <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	632 <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	633 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	634 <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	635 <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	636 <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	637 <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	638 <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	639 <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	640 <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	641 <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	642 <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	643 <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	644 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	645 </output>
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_gene_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="baz" />
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="bar" />
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="2283" />
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="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	654 <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	655 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	656 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	657 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	658 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	659 <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	660 <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	661 <collection type="paired">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	662 <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	663 <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	664 </collection>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	665 </param>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	666 <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	667 <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	668 <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	669 <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	670 <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	671 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	672 <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	673 <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	674 <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	675 <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	676 <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	677 <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	678 <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	679 <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	680 <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	681 <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	682 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	683 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	684 <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	685 <assert_contents>
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="EffectiveLength" />
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="TPM" />
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="baz" />
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="bar" />
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="2283" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	691 <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	692 <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	693 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	694 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	695 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	696 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	697 <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	698 <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	699 <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	700 <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	701 <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	702 <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	703 <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	704 <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	705 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	706 <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	707 <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	708 <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	709 <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	710 <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	711 <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	712 <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	713 <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	714 <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	715 <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	716 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	717 </output>
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_gene_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="baz" />
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="bar" />
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="2283" />
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="1640" />
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	726 <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	727 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	728 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	729 </test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	730 <test>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	731 <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	732 <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	733 <collection type="paired">
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	734 <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	735 <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	736 </collection>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	737 </param>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	738 <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	739 <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	740 <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	741 <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	742 <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	743 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	744 <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	745 <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	746 <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	747 <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	748 <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	749 <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	750 <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	751 <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	752 <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	753 <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	754 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	755 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	756 <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	757 <assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	758 <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	759 <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	760 <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	761 <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	762 <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	763 <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	764 <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	765 </assert_contents>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	766 </output>
d9bfffca4548 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 bgruening parents: 9 diff changeset	767 </test>
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	768 </tests>
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 <help><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	771 What it does
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	772 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	773 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	774 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	775 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	776 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	777 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	778 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	779 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	780 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	781 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	782 (1) Transcript ID,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	783 (2) Transcript Length,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	784 (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	785 (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	786 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	787 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	788 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	789 (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	790
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	791
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	792 Fragment Library Types
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
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	795 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	796 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	797 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	798 (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	799 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	800 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	801 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	802 "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	803 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	804 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	805 illustrated below:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	806 .. image:: ReadLibraryIllustration.png
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	807 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	808 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	809 reads.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	810 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	811 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	812 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	813
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	814 I = inward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	815 O = outward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	816 M = matching
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	817
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	818 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	819 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	820 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	821
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	822 S = stranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	823 U = unstranded
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 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	826 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	827 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	828 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	829 ::
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 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	832 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	833
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	834 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	835 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	836 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	837 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	838 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	839 (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	840 strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	841 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	842 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	843 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	844 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	845 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	846 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	847 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	848
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	849 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	850
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
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	853 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	854
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	855 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	856
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	857 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	858 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	859
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	860 .. 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	861
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	862 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	863 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	864 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	865 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	866
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	867 +---------------------+-------------------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	868 \| 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	869 +=====================+============+============+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	870 \| \| 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	871 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	872 \|``-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	873 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	874 \|``-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	875 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	876 \|``-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	877 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	878
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	879 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	880 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	881 ]]> </help>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	882 <citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	883 <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	884 </citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	885 </tool>

Mercurial > repos > bgruening > salmon

annotate salmon.xml @ 11:c320b539ff54 draft