salmon: salmon.xml annotate

annotate salmon.xml @ 3:0b689bf9473c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f

author	bgruening
date	Thu, 02 Feb 2017 19:37:14 -0500
parents	22cb19d12fcc
children	979bff04ae7d

rev	line source
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	1 <tool id="salmon" name="Salmon" version="0.7.2">
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>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	13 </macros>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	14
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	15 <requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	16 <requirement type="package" version="0.7.2">salmon</requirement>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	17 </requirements>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	18
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	19 <stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	20 <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	21 <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	22 <regex match="Error:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	23 <regex match="Exception:" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	24 <regex match="Exception :" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	25 </stdio>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	26 <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	27 <command><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	28 mkdir ./index
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 mkdir ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	31 #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	32 &&
0 22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	33 salmon index
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	34 --transcripts $refTranscriptSource.ownFile
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	35 --kmerLen $refTranscriptSource.kmerLen
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	36 --threads "\${GALAXY_SLOTS:-4}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	37 --index './index'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	38 --type '$quasi_orphans.type'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	39 $perfectHash
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	40 #if str($sasamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	41 --sasamp $sasamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	42 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	43 #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	44 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	45 #set $index_path = $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	46 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	47 &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	48 #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	49 #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	50 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	51 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	52 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	53 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	54 ln -s $single_or_paired.input_singles ./single.$ext &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	55 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	56 #if $single_or_paired.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	57 #set $ext = 'fasta'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	58 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	59 #set $ext = 'fastq'
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	60 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	61 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	62 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	63 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	64 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	65 ln -s "$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	66 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	67 salmon quant
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	68 --index $index_path
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	69 #if $single_or_paired.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	70 --libType ${single_or_paired.strandedness}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	71 --unmatedReads ./single.$ext
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	72 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	73 --mates1 ./mate1.$ext
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	74 --mates2 ./mate2.$ext
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	75 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	76 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	77 --output ./output
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	78 #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	79 --allowOrphans
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	80 #else:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	81 $quasi_orphans.allowOrphans
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	82 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	83 $seqBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	84 $gcBias
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	85 --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	86 --incompatPrior $adv.incompatPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	87 $adv.consistentHits
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	88 $adv.dumpEq
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	89 #if str($adv.gcSizeSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	90 --gcSizeSamp $adv.gcSizeSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	91 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	92 #if str($adv.biasSpeedSamp):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	93 --biasSpeedSamp $adv.biasSpeedSamp
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	94 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	95 $adv.strictIntersect
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	96 #if str($adv.fldMax):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	97 --fldMax $adv.fldMax
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	98 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	99 #if str($adv.fldMean):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	100 --fldMean $adv.fldMean
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	101 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	102 #if str($adv.fldSD):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	103 --fldSD $adv.fldSD
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	104 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	105 #if $adv.forgettingFactor:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	106 --forgettingFactor $adv.forgettingFactor
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 $adv.writeMappings
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	109 #if str($adv.maxOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	110 --maxOcc $adv.maxOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	111 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	112 $adv.initUniform
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	113 $adv.noFragLengthDist
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	114 $adv.noBiasLengthThreshold
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	115 #if str($adv.maxReadOcc):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	116 --maxReadOcc $adv.maxReadOcc
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	117 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	118 #if $geneMap:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	119 --geneMap ./geneMap.${geneMap.ext}
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	120 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	121 $adv.noEffectiveLengthCorrection
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	122 $adv.useVBOpt
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	123 #if str($adv.numBiasSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	124 --numBiasSamples $adv.numBiasSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	125 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	126 #if str($adv.numAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	127 --numAuxModelSamples $adv.numAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	128 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	129 #if str($adv.numPreAuxModelSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	130 --numPreAuxModelSamples $adv.numPreAuxModelSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	131 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	132 #if str($adv.numGibbsSamples):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	133 --numGibbsSamples $adv.numGibbsSamples
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	134 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	135 #if str($adv.numBootstraps):
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	136 --numBootstraps $adv.numBootstraps
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	137 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	138 $adv.perTranscriptPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	139 #if $adv.vbPrior:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	140 --vbPrior $adv.vbPrior
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	141 #end if
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	142 $adv.writeUnmappedNames
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	143 ]]>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	144 </command>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	145
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	146 <inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	147 <conditional name="refTranscriptSource">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	148 <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	149 <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	150 <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	151 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	152 <when value="indexed">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	153 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	154 <options from_data_table="salmon_indexes">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	155 <filter type="sort_by" column="2"/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	156 <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	157 </options>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	158 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	159 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	160 <when value="history">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	161 <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	162 <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	163 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	164 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	165 <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	166 <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	167 <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	168 <option value="paired">Paired-end</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	169 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	170 <when value="single">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	171 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	172 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	173 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	174 <when value="paired">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	175 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	176 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	177 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	178 <option value="M">Mates are oriented in the same direction (M = matching)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	179 <option value="O">Mates are oriented away from each other (O = outward)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	180 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	181 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	182 <expand macro="strandedness" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	183 </when>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	184 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	185 <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	186 <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	187 <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	188 <option value="fmd">fmd</option>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	189 </param>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	190 <when value="quasi">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	191 </when> <!-- build-in -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	192 <when value="fmd">
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	193 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	194 label="Consider orphaned reads as valid hits when performing lightweight-alignment"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	195 help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	196 </when> <!-- history -->
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	197 </conditional>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	198 <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	199 label="Perfect Hash"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	200 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	201 <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	202 help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	203 <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	204 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	205 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	206 <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	207 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	208 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	209 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	210 label="File containing a mapping of transcripts to genes. 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." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	211 <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	212 <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	213 label="Write Mappings"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	214 help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	215 <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	216 label="Incompatible Prior"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	217 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	218 <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	219 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	220 <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	221 label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	222 <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	223 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	224 <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	225 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	226 <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	227 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	228 <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	229 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	230 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	231 <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	232 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	233 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	234 <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	235 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	236 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	237 <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	238 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	239 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	240 <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	241 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	242 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	243 <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	244 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	245 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	246 <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	247 label="Standard deviation"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	248 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	249 <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	250 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	251 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	252 <param argument="--maxOcc" type="integer" value="200" optional="True"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	253 label="(S)MEMs occuring more than this many times won't be considered"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	254 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	255 <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	256 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	257 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	258 <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	259 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	260 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	261 <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	262 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	263 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	264 <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	265 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	266 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	267 <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	268 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	269 help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	270 <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	271 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	272 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	273 <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	274 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	275 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	276 <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	277 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	278 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	279 <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	280 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	281 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	282 <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	283 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	284 help="This can improve the fragment hit-rate, but is usually not necessary."/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	285 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	286 label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	287 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	288 <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	289 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	290 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	291 <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	292 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	293 help="" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	294 <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	295 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	296 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	297 <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	298 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	299 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	300 <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	301 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	302 help=""/>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	303 </section>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	304 </inputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	305
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	306 <outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	307 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	308 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${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	309 <filter>geneMap</filter>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	310 </data>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	311 </outputs>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	312
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	313 <tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	314 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	334 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	335 </test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	336 <test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	356 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	357 <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	358 <assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	359 <has_text text="EffectiveLength" />
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 </assert_contents>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	367 </output>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	368 </test>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	369 </tests>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	370
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	371 <help><![CDATA[
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	372 What it does
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	373 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	374 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	375 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	376 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	377 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	378 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	379 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	380 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	381 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	382 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	383 (1) Transcript ID,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	384 (2) Transcript Length,
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	385 (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	386 (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	387 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	388 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	389 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	390 (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	391
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	392
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	393 Fragment Library Types
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	394 ======================
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	395
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	396 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	397 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	398 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	399 (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	400 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	401 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	402 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	403 "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	404 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	405 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	406 illustrated below:
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	407 .. image:: ReadLibraryIllustration.png
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	408 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	409 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	410 reads.
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	411 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	412 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	413 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	414
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	415 I = inward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	416 O = outward
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	417 M = matching
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	418
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	419 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	420 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	421 ::
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 S = stranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	424 U = unstranded
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	425
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	426 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	427 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	428 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	429 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	430 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	431
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	432 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	433 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	434
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	435 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	436 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	437 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	438 ISF`` on the command line. This designates that the library being processed has
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	439 the type "ISF" meaning, I\ nward (the relative orientation), S\ tranted
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	440 (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	441 strand).
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	442 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	443 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	444 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	445 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	446 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	447 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	448 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	449
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	450 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	451
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	452 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	453
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	454 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	455
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	456 ::
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	457
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	458 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	459 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	460
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	461 .. 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	462
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	463 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	464 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	465 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	466 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	467
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	468 +---------------------+-------------------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	469 \| 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	470 +=====================+============+============+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	471 \| \| 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	472 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	473 \|``-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	474 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	475 \|``-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	476 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	477 \|``-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	478 +---------------------+------------+------------+
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	479
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	480 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	481 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	482 ]]> </help>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	483 <citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	484 <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	485 </citations>
22cb19d12fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 49aa400dbbcab6ce76272d8b05df6981a5307783-dirty bgruening parents: diff changeset	486 </tool>

Mercurial > repos > bgruening > salmon

annotate salmon.xml @ 3:0b689bf9473c draft