Mercurial > repos > drosofff > msp_sr_bowtie
changeset 38:0d961f45e43e draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b5e020763495240ddb730f757f0f30cafd208a6b-dirty
| author | drosofff |
|---|---|
| date | Sun, 02 Jul 2017 17:10:28 -0400 |
| parents | 7128df6248e5 |
| children | 97f256cbdaf6 |
| files | sRbowtie.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/sRbowtie.xml Sun Jul 02 16:41:35 2017 -0400 +++ b/sRbowtie.xml Sun Jul 02 17:10:28 2017 -0400 @@ -1,8 +1,8 @@ <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2"> <description>for FASTA small reads</description> <requirements> - <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="package" version="1.3.1=py27_0">samtools</requirement> + <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> + <requirement type="package" version="1.2">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $refGenomeSource.genomeSource == "history": @@ -50,7 +50,7 @@ #elif $output_format == "sam": bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' #elif $output_format == "bam": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output #end if ##### | samtools view -uS ]]></command>