comparison macros.xml @ 1:1930eb870dca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"

0:ad69d2a05c3c

                <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;" />

            </mapping>
       </sanitizer>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.5969107</citation>
        </citations>
    </xml>
</macros>

1:1930eb870dca

                <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="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="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;" />

            </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>