Mercurial > repos > mvdbeek > samblaster

changeset 1:4f68e55100c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
author mvdbeek
date Fri, 16 Dec 2016 05:44:40 -0500
parents 5743b5c0209b
children 5d1a1388a036
files samblaster.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/samblaster.xml	Fri Dec 16 04:45:26 2016 -0500
+++ b/samblaster.xml	Fri Dec 16 05:44:40 2016 -0500
@@ -1,11 +1,11 @@
-<tool id="samblaster" name="samblaster" version="0.1.24">
+<tool id="samblaster" name="samblaster" version="0.1.24.1">
     <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
     <requirements>
         <requirement type="package" version="0.1.24">samblaster</requirement>
         <requirement type="package" version="1.3.1">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        samtools sort -O sam -n '$input' |
+        samtools sort -@ \$GALAXY_SLOTS:-4 -m 4G -O sam -n '$input' |
         samblaster
         $output
         $discordantFile
@@ -24,9 +24,9 @@
     ]]></command>
     <inputs>
         <param name="input" argument="--input" type="data" format="bam,sam"/>
-        <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -O bam -o output.bam)" falsevalue="-o /dev/null"/>
-        <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -O bam -o discordant.bam)" falsevalue=""/>
-        <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -O bam -o splitter.bam)" falsevalue=""/>
+        <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o output.bam)" falsevalue="-o /dev/null"/>
+        <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o discordant.bam)" falsevalue=""/>
+        <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o splitter.bam)" falsevalue=""/>
         <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>
         <param name="acceptDupMarks" argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/>
         <param name="excludeDups" argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/>