comparison bismark_bowtie2_wrapper.xml @ 3:91f07ff056ca draft

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2:82814a8a2395

<tool id="bismark_bowtie2" name="Bismark" version="0.7.12.1">
    <!-- Wrapper compatible with Bismark version 0.7.11 -->
    <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>

    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_wrapper.py
        
        ## Change this to accommodate the number of threads you have available.
        --num-threads 24

        --bismark_path \$SCRIPT_PATH

        --bowtie2

            -I $singlePaired.minInsert
            -X $singlePaired.maxInsert
        #end if


        ## for now hardcode the value for the required memory per thread in --best mode
        --chunkmbs 512

                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
            </when>
        </conditional>


        <conditional name="params">
            <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
              <option value="default">Use Defaults</option>
              <option value="custom">Full parameter list</option>

            </action>
          </when>
        </conditional>
      </actions>
    </data>
        
        
    </outputs>

    <tests>
    </tests>

3:91f07ff056ca

<tool id="bismark_bowtie2" name="Bismark" version="0.10.1">
    <!-- 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>

    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_wrapper.py
        
        ## Change this to accommodate the number of threads you have available.
        --num-threads "\${GALAXY_SLOTS:-24}"

        --bismark_path \$SCRIPT_PATH

        --bowtie2

            -I $singlePaired.minInsert
            -X $singlePaired.maxInsert
        #end if

        #if $sort_bam:
            --sort-bam
        #end if

        ## for now hardcode the value for the required memory per thread in --best mode
        --chunkmbs 512

                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
            </when>
        </conditional>

        <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>

        <conditional name="params">
            <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
              <option value="default">Use Defaults</option>
              <option value="custom">Full parameter list</option>

            </action>
          </when>
        </conditional>
      </actions>
    </data>
    </outputs>

    <tests>
    </tests>