annotate macros.xml @ 0:ad69d2a05c3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"

<macros>
    <token name="@TOOL_VERSION@">6.21.7</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.09</token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">megan</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
        </requirements>
    </xml>
    <macro name="input_type_cond">
        <conditional name="input_type_cond">
            <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
                <option value="single" selected="true">Single dataset</option>
                <option value="pair">Dataset pair</option>
                <option value="paired">List of dataset pairs</option>
            </param>
            <when value="single">
                <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
            </when>
            <when value="pair">
                <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
                <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
                <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
                <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
                <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
                <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
            </when>
        </conditional>
    </macro>
    <macro name="blast_mode_options">
        <option value="Unknown" selected="true">Unknown</option>
        <option value="BlastN">BlastN</option>
        <option value="BlastP">BlastP</option>
        <option value="BlastX">BlastX</option>
        <option value="Classifier">Classifier</option>
    </macro>
    <macro name="common_blast_params">
        <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
        <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
        <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
        <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
    </macro>
    <xml name="sanitize_query" token_validinitial="string.printable">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <remove value="&apos;" />
                <add value="|" />
            </valid>
            <mapping initial="none">
                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
            </mapping>
       </sanitizer>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.5969107</citation>
        </citations>
    </xml>
</macros>