Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 19:44959aa06aeb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 27ea73be9aede1e0939ecd7c5f560ac2a630869a"
author iuc
date Fri, 02 Jul 2021 20:18:29 +0000
parents c772497b2c32
children 91e0f03268ca
comparison
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18:c772497b2c32 19:44959aa06aeb
1 <tool id="rna_star" name="RNA STAR" version="@VERSION@" profile="20.01" license="MIT"> 1 <tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy0" profile="20.01" license="MIT">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">star</xref> 4 <xref type="bio.tools">star</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
208 #end if 208 #end if
209 #end if 209 #end if
210 210
211 --outBAMsortingThreadN \${GALAXY_SLOTS:-4} 211 --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
212 --outBAMsortingBinsN $perf.outBAMsortingBinsN 212 --outBAMsortingBinsN $perf.outBAMsortingBinsN
213 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
213 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000)) 214 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
214 215
215 ## Handle chimeric options and output 216 ## Handle chimeric options and output
216 #if str($chimOutType): 217 #if str($chimOutType):
217 --chimOutType $chimOutType 218 --chimOutType $chimOutType
498 </when> 499 </when>
499 </conditional> 500 </conditional>
500 </section> 501 </section>
501 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false"> 502 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false">
502 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." /> 503 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." />
504 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" />
503 </section> 505 </section>
504 </inputs> 506 </inputs>
505 507
506 <outputs> 508 <outputs>
507 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> 509 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">