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comparison sailfish.xml @ 4:03c74355227f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit edee3afc7d729be9a224d21729bb7490a3761a0e
author bgruening
date Sun, 18 Sep 2016 06:05:57 -0400
parents 20eab032389f
children 1b4ed566a41c
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3:85d0d479f05b 4:03c74355227f
1 <tool id="sailfish" name="Sailfish" version="0.7.6.0"> 1 <tool id="sailfish" name="Sailfish" version="0.7.6.1">
2 <description>transcript quantification from RNA-seq data</description> 2 <description>transcript quantification from RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.6">sailfish</requirement> 4 <requirement type="package" version="0.7.6">sailfish</requirement>
5 <requirement type="package" version="1.57.0">boost</requirement>
5 </requirements> 6 </requirements>
6 <macros> 7 <macros>
7 <xml name="strandedness"> 8 <xml name="strandedness">
8 <param name="strandedness" type="select" label="Specify the strandedness of the reads"> 9 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
9 <option value="U" selected="True">Not stranded (U)</option> 10 <option value="U" selected="True">Not stranded (U)</option>
70 #else: 71 #else:
71 --mates1 ./mate1.$ext 72 --mates1 ./mate1.$ext
72 --mates2 ./mate2.$ext 73 --mates2 ./mate2.$ext
73 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" 74 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
74 #end if 75 #end if
75 --output ./ 76 --output ./
76 $biasCorrect 77 $biasCorrect
77 --threads "\${GALAXY_SLOTS:-4}" 78 --threads "\${GALAXY_SLOTS:-4}"
78 79
79 #if $fldMean: 80 #if $fldMean:
80 --fldMean $fldMean 81 --fldMean $fldMean
115 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 116 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
116 </options> 117 </options>
117 </param> 118 </param>
118 </when> <!-- build-in --> 119 </when> <!-- build-in -->
119 <when value="history"> 120 <when value="history">
120 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" /> 121 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" help="in FASTA format" />
121 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built" 122 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built"
122 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. 123 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
123 The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, 124 The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers,
124 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/> 125 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/>
125 </when> <!-- history --> 126 </when> <!-- history -->
126 </conditional> <!-- refTranscriptSource --> 127 </conditional> <!-- refTranscriptSource -->
127 128
206 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_bias_corrected_quant" /> 207 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_bias_corrected_quant" />
207 </test> 208 </test>
208 </tests> 209 </tests>
209 <help> 210 <help>
210 <![CDATA[ 211 <![CDATA[
212
211 **What it does** 213 **What it does**
212 214
213 Sailfish is a tool for transcript quantification from RNA-seq data. It 215 Sailfish is a tool for transcript quantification from RNA-seq data. It
214 requires a set of target transcripts (either from a reference or de-novo 216 requires a set of target transcripts (either from a reference or de-novo
215 assembly) to quantify. All you need to run Sailfish is a fasta file containing 217 assembly) to quantify. All you need to run Sailfish is a fasta file containing
308 :: 310 ::
309 311
310 OSR (a stranded paired-end protocol where the reads face away from each other, 312 OSR (a stranded paired-end protocol where the reads face away from each other,
311 read1 comes from reverse strand and read2 comes from the forward strand) 313 read1 comes from reverse strand and read2 comes from the forward strand)
312 314
313 .. note:: Correspondence to TopHat library types 315 .. note:: Correspondence to TopHat library types
314 316
315 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq 317 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
316 read aligner has a different convention for specifying the format of the library. 318 read aligner has a different convention for specifying the format of the library.
317 Below is a table that provides the corresponding sailfish/salmon library format 319 Below is a table that provides the corresponding sailfish/salmon library format
318 string for each of the potential TopHat library types: 320 string for each of the potential TopHat library types:
319 321
320 322
321 +---------------------+-------------------------+ 323 +---------------------+-------------------------+
322 | TopHat | Salmon (and Sailfish) | 324 | TopHat | Salmon (and Sailfish) |
323 +=====================+============+============+ 325 +=====================+============+============+
324 | | Paired-end | Single-end | 326 | | Paired-end | Single-end |
325 +---------------------+------------+------------+ 327 +---------------------+------------+------------+
326 |``-fr-unstranded`` |``-l IU`` |``-l U`` | 328 |``-fr-unstranded`` |``-l IU`` |``-l U`` |
327 +---------------------+------------+------------+ 329 +---------------------+------------+------------+
328 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` | 330 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
329 +---------------------+------------+------------+ 331 +---------------------+------------+------------+