annotate lastz_macros.xml @ 10:3e1ea2facca6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"

<macros>
    <token name="@TOOL_VERSION@">1.04.15</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[
        #if $source.ref_source=="history":
            #if $source.target.is_of_type('fasta.gz'):
                <(gunzip -c '${source.target}')
            #else:
                '${source.target}'
            #end if
        #else:
            '${source.target_2bit.fields.path}'
        #end if
        ]]>
    </token>
    <token name="@query_input@"><![CDATA[
        #if $query.is_of_type('fasta.gz','fastq.gz'):
            <(gunzip -c '${query}')
        #elif $query.is_of_type('fastq.bz2'):
            <(bunzip2 -c '${query}')
        #else:
            '${query}'
        #end if
        ]]>
    </token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">lastz</xref>
        </xrefs>
    </xml>
    <xml name="target_input">
        <conditional name="source">
            <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option">
                <option value="cached">locally cached</option>
                <option value="history">from your history</option>
            </param>
            <when value="cached">
                <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                    <options from_data_table="lastz_seqs" />
                </param>
            </when>
            <when value="history">
                <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" />
            </when>
        </conditional>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
            @misc{
                githublastz,
                author = {Harris, Robert},
                year = {2007},
                title = {Improved pairwise alignment of genomic DNA},
                publisher = {The Pennsylvania State University},
                journal = {Ph. D. Thesis},
                url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf},
                }
            </citation>
        </citations>
    </xml>
</macros>