annotate macros.xml @ 2:07d36bc47eaf draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"

<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="input_daa_param">
        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
    </macro>
    <macro name="long_reads_param">
        <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
    </macro>
    <macro name="max_matches_per_read_param">
        <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
    </macro>
    <macro name="only_named_classifications_param">
        <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
            <sanitizer>
                <valid initial="@VALIDINITIAL@">
                    <remove value="&apos;" />
                    <add value="|" />
                </valid>
                <mapping initial="none">
                    <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
                </mapping>
            </sanitizer>
        </param>
    </macro>
    <macro name="classification_options">
        <option value="EC" selected="true">EC</option>
        <option value="EGGNOG">EGGNOG</option>
        <option value="GTDB">GTDB</option>
        <option value="INTERPRO2GO">INTERPRO2GO</option>
        <option value="KEGG">KEGG</option>
        <option value="SEED">SEED</option>
        <option value="Taxonomy">Taxonomy</option>
    </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="classify_param">
        <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
    </macro>
    <macro name="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>
    <macro name="min_max_params">
        <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
        <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
        <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
        <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
        <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
    </macro>
    <macro name="lca_params">
        <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
            <option value="naive" selected="true">naive</option>
            <option value="weighted">weighted</option>
            <option value="longReads">longReads</option>
        </param>
        <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
    </macro>
    <macro name="read_assignment_mode_param">
        <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
            <option value="alignedBases" selected="true">alignedBases</option>
            <option value="readCount">readCount</option>
        </param>
    </macro>
    <macro name="con_file_param">
        <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>
    </macro>
    <macro name="mapdb_param">
        <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
    </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">10.1038/nmeth.3176</citation>
            <citation type="doi">10.1101/gr.120618.111</citation>
            <citation type="doi">10.1101/gr.5969107</citation>
        </citations>
    </xml>
</macros>