comparison bowtie2_wrapper.xml @ 26:09b2cdb7ace5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"

25:749c918495f7

<tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.3.4.1">bowtie2</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

    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} -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view -bS - -o '$output'
#else:
    > '$output'
#end if

26:09b2cdb7ace5

<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>
        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
        <requirement type="package" version="1.11">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

    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