comparison bismark_bowtie2_wrapper.xml @ 22:047eb877b6f0 draft

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21:507901240749

<tool id="bismark_bowtie2" name="Bismark" version="0.10.2">
    <!-- Wrapper compatible with Bismark version 0.10 -->
    <description>bisulfite mapper (bowtie2)</description>
    <!--<version_command>bismark version</version_command>-->
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />

        bismark_wrapper.py

        ## Change this to accommodate the number of threads you have available.
        --num-threads "\${GALAXY_SLOTS:-24}"

        --bismark_path \$SCRIPT_PATH

        --bowtie2

        ##
        ## Bismark Genome Preparation, if desired.

22:047eb877b6f0

<tool id="bismark_bowtie2" name="Bismark" version="0.14.3">
    <!-- Wrapper compatible with Bismark version 0.10 -->
    <description>bisulfite mapper (bowtie2)</description>
    <!--<version_command>bismark version</version_command>-->
    <requirements>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.2.5">bowtie2</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />

        bismark_wrapper.py

        ## Change this to accommodate the number of threads you have available.
        --num-threads "\${GALAXY_SLOTS:-24}"

        --bismark_path $__tool_directory__

        --bowtie2

        ##
        ## Bismark Genome Preparation, if desired.