Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 6:2055c2667eb3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 427913231c5894bde2b2ed428da2b8aee30bc311
author iuc
date Thu, 01 Mar 2018 11:56:28 -0500
parents 99b17b74a8cd
children a70a7eebb435
comparison
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5:99b17b74a8cd 6:2055c2667eb3
1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01"> 1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
118 --chimSegmentMin 12 118 --chimSegmentMin 12
119 --chimJunctionOverhangMin 12 119 --chimJunctionOverhangMin 12
120 --alignSJDBoverhangMin 10 120 --alignSJDBoverhangMin 10
121 --alignMatesGapMax 200000 121 --alignMatesGapMax 200000
122 --alignIntronMax 200000 122 --alignIntronMax 200000
123 123 --twopassMode Basic
124 ## --twopass1readsN 100000000 124 --twopass1readsN -1
125
125 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0 126 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
126 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0 127 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
127 128
128 #elif str( $params.settingsType ) == "full": 129 #elif str( $params.settingsType ) == "full":
129 ## Extended parameter options 130 ## Extended parameter options
147 --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate" 148 --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
148 --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax" 149 --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
149 --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax" 150 --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
150 --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax" 151 --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
151 --alignEndsType $params.align.alignEndsType 152 --alignEndsType $params.align.alignEndsType
153
154 ## Two pass mode
155 --twopassMode "$params.twopass.twopassMode"
156 #if str( $params.twopass.twopassMode ) == "Basic":
157 --twopass1readsN "$params.twopass.twopass1readsN"
158 #end if
152 159
153 ## Chimeric alignment parameter options 160 ## Chimeric alignment parameter options
154 #if str( $params.chim.chim_select ) == "yes": 161 #if str( $params.chim.chim_select ) == "yes":
155 --chimSegmentMin "$params.chim.chimSegmentMin" 162 --chimSegmentMin "$params.chim.chimSegmentMin"
156 --chimScoreMin "$params.chim.chimScoreMin" 163 --chimScoreMin "$params.chim.chimScoreMin"
323 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> 330 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
324 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> 331 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
325 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/> 332 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
326 </section> 333 </section>
327 334
335 <section name="twopass" title="Two pass mode" expanded="False">
336 <param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/>
337 <param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/>
338 </section>
339
328 <section name="limits" title="Limits" expanded="False"> 340 <section name="limits" title="Limits" expanded="False">
329 <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." /> 341 <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
330 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" /> 342 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
331 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" /> 343 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
332 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." /> 344 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
333 </section> 345 </section>
334 346
335 <conditional name="chim"> 347 <conditional name="chim">
336 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?"> 348 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
337 <option value="no" selected="true">No</option> 349 <option value="no" selected="true">No</option>
569 **STAR-Fusion** 581 **STAR-Fusion**
570 582
571 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running 583 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
572 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions:: 584 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
573 585
574 --twopassMode Basic # not an option in STAR 2.4.0
575 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0 586 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
576 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0 587 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
577 588
578 **Attributions** 589 **Attributions**
579 590