comparison bowtie2_wrapper.xml @ 28:8681e741a037 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"

27:c9105910063f

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>

    2> '$mapping_stats'
#end if

## output file
#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view -bS - -o '$output'
#else:
    > '$output'
#end if

## rename unaligned sequence files

28:8681e741a037

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>

    2> '$mapping_stats'
#end if

## output file
#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view --no-PG -bS - -o '$output'
#else:
    > '$output'
#end if

## rename unaligned sequence files