Mercurial > repos > drosofff > msp_sr_bowtie
diff sRbowtie.xml @ 18:9fe34d55bfb0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 083e56a5896485479dfd679e0b571eb2bd8aed0b
| author | drosofff |
|---|---|
| date | Mon, 26 Jun 2017 19:49:25 -0400 |
| parents | 0806b5d0b5da |
| children | dd5985c5798d |
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--- a/sRbowtie.xml Mon Jun 26 19:37:53 2017 -0400 +++ b/sRbowtie.xml Mon Jun 26 19:49:25 2017 -0400 @@ -8,7 +8,7 @@ #if $refGenomeSource.genomeSource == "history": bowtie-build -f '$refGenomeSource.ownFile' local_index && #else: - ln -s local_index '$refGenomeSource.index.fields.path' && + ln -f -s '$refGenomeSource.index.fields.path' local_index && #end if #if $input.extension == "fasta": #set format = "-f" @@ -42,15 +42,15 @@ #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned)) #end if - #set $method_postfix = "$method_prefix" + "$extra_output" + #set $method_postfix = " %s %s " % ($method_prefix", "$extra_output") ## run the bowtie alignement #if $output_format == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --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_prefix $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_prefix $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 view -bS - > $output #end if ]]></command>