Mercurial > repos > drosofff > msp_sr_bowtie
changeset 29:04685a1b3de1 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
| author | drosofff |
|---|---|
| date | Sun, 02 Jul 2017 12:34:18 -0400 |
| parents | c1ae0c9ad7d1 |
| children | 5bd8c555390d |
| files | sRbowtie.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/sRbowtie.xml Sun Jul 02 12:22:16 2017 -0400 +++ b/sRbowtie.xml Sun Jul 02 12:34:18 2017 -0400 @@ -5,7 +5,7 @@ <requirement type="package" version="1.4.1">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - #if str($refGenomeSource.genomeSource) == "history": + #if $refGenomeSource.genomeSource == "history": bowtie-build -f $refGenomeSource.ownFile local_index && #else: ln -f -s $refGenomeSource.index.fields.path local_index && @@ -45,11 +45,11 @@ #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) ## run the bowtie alignement - #if str($output_format) == "tabular": + #if $output_format == "tabular": bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > '$output' - #elif str($output_format) == "sam": + #elif $output_format == "sam": bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' - #elif str($output_format) == "bam": + #elif $output_format == "bam": bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output' #end if ##### | samtools view -uS