Mercurial > repos > drosofff > msp_sr_bowtie
diff sRbowtie.xml @ 24:2f4e22f2177d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit cc96644a48fed1476e854fb7116b5f51c42f9f17
| author | drosofff |
|---|---|
| date | Wed, 28 Jun 2017 17:45:25 -0400 |
| parents | 411b6453b5d0 |
| children | 592eab0f31ac |
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--- a/sRbowtie.xml Tue Jun 27 04:49:57 2017 -0400 +++ b/sRbowtie.xml Wed Jun 28 17:45:25 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="1.2">samtools</requirement> + <requirement type="package" version="1.2">bowtie</requirement> + <requirement type="package" version="1.4.1">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($refGenomeSource.genomeSource) == "history": @@ -46,11 +46,11 @@ ## run the bowtie alignement #if $output_format == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' --suppress 6,7,8 '${extra_output}' local_index '${format}' '$input' > '$output' + bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' --suppress 6,7,8 '$extra_output' local_index '$format' '$input' > '$output' #elif $output_format == "sam": - bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input > $output + bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output #elif $output_format == "bam": - bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input |samtools view -bS - > $output + bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools sort -O bam -o '$output' #end if ]]></command>