Mercurial > repos > iuc > rgrnastar
changeset 6:2055c2667eb3 draft
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 |
| files | rg_rnaStar.xml |
| diffstat | 1 files changed, 17 insertions(+), 6 deletions(-) [+] |
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--- a/rg_rnaStar.xml Thu Oct 12 04:59:08 2017 -0400 +++ b/rg_rnaStar.xml Thu Mar 01 11:56:28 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01"> +<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01"> <description>Gapped-read mapper for RNA-seq data</description> <macros> <import>macros.xml</import> @@ -120,8 +120,9 @@ --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 + --twopassMode Basic + --twopass1readsN -1 - ## --twopass1readsN 100000000 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0 @@ -150,6 +151,12 @@ --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax" --alignEndsType $params.align.alignEndsType + ## Two pass mode + --twopassMode "$params.twopass.twopassMode" + #if str( $params.twopass.twopassMode ) == "Basic": + --twopass1readsN "$params.twopass.twopass1readsN" + #end if + ## Chimeric alignment parameter options #if str( $params.chim.chim_select ) == "yes": --chimSegmentMin "$params.chim.chimSegmentMin" @@ -325,11 +332,16 @@ <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="twopass" title="Two pass mode" expanded="False"> + <param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/> + <param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/> + </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." /> + <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"> @@ -571,7 +583,6 @@ STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running STAR prior to STAR-Fusion can be pre-selected, with the following exceptions:: - --twopassMode Basic # not an option in STAR 2.4.0 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0