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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf |
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modified:
rg_rnaStar.xml |
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| diff -r d681e989ac95 -r 99b17b74a8cd rg_rnaStar.xml --- a/rg_rnaStar.xml Fri Jun 09 07:34:30 2017 -0400 +++ b/rg_rnaStar.xml Thu Oct 12 04:59:08 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01"> +<tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01"> <description>Gapped-read mapper for RNA-seq data</description> <macros> <import>macros.xml</import> @@ -159,6 +159,13 @@ --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG" --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin" #end if + + ## Limits + --limitBAMsortRAM "$params.limits.limitBAMsortRAM" + --limitOutSJoneRead "$params.limits.limitOutSJoneRead" + --limitOutSJcollapsed "$params.limits.limitOutSJcollapsed" + --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj" + #end if ## Convert chimeric reads. @@ -285,7 +292,7 @@ <!-- Other parameter settings. --> <conditional name="params"> - <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)"> + <param name="settingsType" type="select" label="Other parameters (seed, alignment, limits and chimeric alignment)"> <option value="default" selected="true">Use Defaults</option> <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> <option value="full">Extended parameter list</option> @@ -317,6 +324,13 @@ <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/> </section> + + <section name="limits" title="Limits" expanded="False"> + <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." /> + <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" /> + <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" /> + <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." /> + </section> <conditional name="chim"> <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?"> |