Mercurial > repos > devteam > bowtie2
changeset 4:1fc845afa3ac draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 13:00:51 -0400 |
| parents | ceb6467e276c |
| children | 42bb952b4e3c |
| files | bowtie2_wrapper.xml |
| diffstat | 1 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/bowtie2_wrapper.xml Mon Mar 09 11:58:43 2015 -0400 +++ b/bowtie2_wrapper.xml Tue Jul 21 13:00:51 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="0.4"> +<tool id="bowtie2" name="Bowtie2" version="0.5"> <!-- Wrapper compatible with Bowtie version 2.2.4 --> <description>- map reads against reference genome</description> <version_command>bowtie2 --version</version_command> @@ -145,18 +145,19 @@ #elif str( $analysis_type.analysis_type_selector ) == "cline": ${analysis_type.cline} - #end if + #end if + -S "galaxy_bowtie_2_output.sam" && + ## view/sort and output BAM file - | samtools view -Su - | samtools sort -o - - > $output + ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output ) ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: - #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) - #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - - ; mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r + #from os.path import splitext + #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) + && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }" + && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }" #end if </command>