comparison flexbar_dsc.xml @ 29:65103aba4e5f draft

fix xml

28:3d608b751bc4

    <requirements>
        <requirement type="package" version="2.5">flexbar</requirement>
    </requirements>

    <version_command>flexbar --version</version_command>

        flexbar

        --threads \${GALAXY_SLOTS:-1}

        #end if

        --target FlexbarOutput &&
        for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done &&
        for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done



    </command>


    <inputs>

        <param format="fastq,fastqsanger,fastqsolexa,fastqillumina,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>

           identifier in the nested collection and identifier_1 is either
           forward or reverse (for instance samp1_forward.fq).
      -->
        <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" />
        <!--<data format="txt" name="output" metadata_source="reads"/>-->
    </outputs>


    <help>

29:65103aba4e5f

    <requirements>
        <requirement type="package" version="2.5">flexbar</requirement>
    </requirements>

    <version_command>flexbar --version</version_command>

    <command><![CDATA[

        flexbar

        --threads \${GALAXY_SLOTS:-1}

        #end if

        --target FlexbarOutput &&
        for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done &&
        for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done
    ]]></command>


    <inputs>

        <param format="fastq,fastqsanger,fastqsolexa,fastqillumina,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>

           identifier in the nested collection and identifier_1 is either
           forward or reverse (for instance samp1_forward.fq).
      -->
        <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" />
        <!--<data format="txt" name="output" metadata_source="reads"/>-->
        </collection>
    </outputs>


    <help>