Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 5:99b17b74a8cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
author iuc
date Thu, 12 Oct 2017 04:59:08 -0400
parents 318b2a9d54dd
children 2055c2667eb3
comparison
equal deleted inserted replaced
4:d681e989ac95 5:99b17b74a8cd
1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01"> 1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-1" 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"/>
157 --chimScoreDropMax "$params.chim.chimScoreDropMax" 157 --chimScoreDropMax "$params.chim.chimScoreDropMax"
158 --chimScoreSeparation "$params.chim.chimScoreSeparation" 158 --chimScoreSeparation "$params.chim.chimScoreSeparation"
159 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG" 159 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
160 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin" 160 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
161 #end if 161 #end if
162
163 ## Limits
164 --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
165 --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
166 --limitOutSJcollapsed "$params.limits.limitOutSJcollapsed"
167 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"
168
162 #end if 169 #end if
163 170
164 ## Convert chimeric reads. 171 ## Convert chimeric reads.
165 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ): 172 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
166 && 173 &&
283 <when value="no"/> 290 <when value="no"/>
284 </conditional> 291 </conditional>
285 292
286 <!-- Other parameter settings. --> 293 <!-- Other parameter settings. -->
287 <conditional name="params"> 294 <conditional name="params">
288 <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)"> 295 <param name="settingsType" type="select" label="Other parameters (seed, alignment, limits and chimeric alignment)">
289 <option value="default" selected="true">Use Defaults</option> 296 <option value="default" selected="true">Use Defaults</option>
290 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> 297 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
291 <option value="full">Extended parameter list</option> 298 <option value="full">Extended parameter list</option>
292 </param> 299 </param>
293 <when value="default"/> 300 <when value="default"/>
315 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/> 322 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
316 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> 323 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
317 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> 324 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
318 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/> 325 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
319 </section> 326 </section>
327
328 <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." />
330 <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" />
332 <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>
320 334
321 <conditional name="chim"> 335 <conditional name="chim">
322 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?"> 336 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
323 <option value="no" selected="true">No</option> 337 <option value="no" selected="true">No</option>
324 <option value="yes">Yes</option> 338 <option value="yes">Yes</option>