Mercurial > repos > artbio > sr_bowtie
changeset 1:5f4fbba31b6a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 2dac5b5f1ed589f4c8a3c6d64696b842ece8edd2
author | artbio |
---|---|
date | Wed, 11 Oct 2017 06:01:15 -0400 |
parents | de9cd3998571 |
children | 304adcfe3660 |
files | sRbowtie.xml |
diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/sRbowtie.xml Sat Sep 02 10:52:05 2017 -0400 +++ b/sRbowtie.xml Wed Oct 11 06:01:15 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.0"> +<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.1"> <description>for small RNA short reads</description> <requirements> <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> @@ -6,7 +6,7 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ #if $refGenomeSource.genomeSource == "history": - bowtie-build -f $refGenomeSource.ownFile genome && + bowtie-build -f $refGenomeSource.ownFile genome 1>/dev/null && ln -s -f '$refGenomeSource.ownFile' genome.fa && #set index_path = 'genome' #else: @@ -48,11 +48,11 @@ ## run the bowtie alignement #if $output_format == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' 2>&1 > $output #elif $output_format == "sam": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output' + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' 2>&1 > '$output' #elif $output_format == "bam": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input'| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output 2>&1 #end if ##### | samtools view -uS ]]></command>