comparison bowtie2_wrapper.xml @ 4:1fc845afa3ac draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty

3:ceb6467e276c

<tool id="bowtie2" name="Bowtie2" version="0.4">
    <!-- Wrapper compatible with Bowtie version 2.2.4 -->
    <description>- map reads against reference genome</description>
    <version_command>bowtie2 --version</version_command>
    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>

                --seed "${analysis_type.other_options.seed}"
            #end if
        
        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #end if    
        
        ## view/sort and output BAM file
        | samtools view -Su - | 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
        #end if
        
    </command>
    
    <!-- basic error handling -->

4:1fc845afa3ac

<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>
    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>

                --seed "${analysis_type.other_options.seed}"
            #end if
        
        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #end if
        
        -S "galaxy_bowtie_2_output.sam" &&

        ## view/sort and output BAM file
        ( 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:
            #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>
    
    <!-- basic error handling -->