<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8">
    <requirements>
        <requirement type="package" >homer</requirement>
    </requirements>
    <description>makeTagDirectory</description>
    <version_command>echo "Doh!"</version_command>
    <command> makeTagDirectory ${tagDir.extra_files_path}
        #for $alignF in $alignmentFiles
          $alignF.file -format $alignF.file.ext
        #end for
        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2

    </command>
    <inputs>
        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
        <repeat name="alignmentFiles" title="Alignment Files">
          <param name="file" label="Add file" type="data" format="sam,bed" />
        </repeat>
    </inputs>
    <outputs>
        <data format="homerTagDirectory" name="tagDir" label="${title}" />
        <data format="txt" name="out_log" label="${title}.log" />
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
    </outputs>


    <tests>
        <!--<test>-->
            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
        <!--</test>-->
    </tests>

    <help>

        .. class:: infomark

        After the job finishes, save the zip file, unzip and open "index.html"

        The actual meme-chip command is displayed under "Command line summary"

        Defaults:
        http://meme.nbcr.net/meme/doc/meme-chip.html

    </help>
</tool>