Mercurial > repos > drosofff > msp_sr_bowtie
changeset 15:44d61fa7fb75 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
| author | drosofff |
|---|---|
| date | Mon, 26 Jun 2017 15:18:23 -0400 |
| parents | a05b107fd0c4 |
| children | 57b6452f9d76 |
| files | sRbowtie.xml |
| diffstat | 1 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/sRbowtie.xml Mon Jun 26 12:06:12 2017 -0400 +++ b/sRbowtie.xml Mon Jun 26 15:18:23 2017 -0400 @@ -35,20 +35,22 @@ #if $additional_fasta == "No": #set extra_output = "" #elif $additional_fasta == "al": - #set extra_output = " --un %s" % str(unaligned) + #set extra_output = " --al %s " % str($aligned) + #elif $additional_fasta == "unal": + #set extra_output = " --un %s " % str($unaligned) #else: - #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned)) + #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned)) #end if #set $method_postfix = "$method_prefix" + "$extra_output" ## run the bowtie alignement #if $output_format == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 "local_index" $format $input > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 $extra_output$"local_index" $format $input > $output #elif $output_format == "sam": - bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input > $output #elif $output_format == "bam": - bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input |samtools view -bS - > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input |samtools view -bS - > $output #end if ]]></command>