Mercurial > repos > drosofff > msp_sr_bowtie
diff sRbowtie.xml @ 26:405cd77e5a83 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 49b9fd4b6b28a6cbbabc6fa0356cf52be20b7a3e
| author | drosofff |
|---|---|
| date | Fri, 30 Jun 2017 18:46:35 -0400 |
| parents | 592eab0f31ac |
| children | 2578aea69626 |
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--- a/sRbowtie.xml Fri Jun 30 18:12:45 2017 -0400 +++ b/sRbowtie.xml Fri Jun 30 18:46:35 2017 -0400 @@ -45,11 +45,11 @@ #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) ## run the bowtie alignement - #if $output_format == "tabular": + #if str($output_format) == "tabular": bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' --suppress 6,7,8 '$extra_output' local_index '$format' '$input' > '$output' - #elif $output_format == "sam": + #elif str($output_format) == "sam": bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output - #elif $output_format == "bam": + #elif str($output_format) == "bam": bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools view -uS | samtools sort -O bam -o '$output' #end if