comparison macros.xml @ 30:4317d3cb6cba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787

29:6ea73833cf67

<macros>
    <token name="@TOOL_VERSION@">3.0.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->

    </macro>
    <macro name="matepairDist">
        <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
    </macro>
    <macro name="citation">
        <citations>
            <citation type="doi">10.1093/nar/gkq1019</citation>
            <citation type="bibtex">
@misc{github_sratools,

30:4317d3cb6cba

<macros>
    <token name="@TOOL_VERSION@">3.0.5</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->

    </macro>
    <macro name="matepairDist">
        <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
    </macro>
    <macro name="defline" tokens="defline_param,defline_default">
        <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
            <help>A string of characters and/or variables. The variables can be one of:
                $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
                '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
                Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
            <!-- allow many chars, but quotes and backslash -->
            <sanitizer>
                <valid initial="string.ascii_letters,string.digits">
                    <add value="@" />
                    <add value="$" />
                    <add value="[" />
                    <add value="]" />
                    <add value="_" />
                    <add value="-" />
                    <add value="+" />
                    <add value="." />
                    <add value=";" />
                    <add value=":" />
                    <add value="/" />
                    <add value="?" />
                </valid>
            </sanitizer>
            <validator type="regex" message="Must start with @">^.*</validator>

        </param> 
    </macro>
    <macro name="citation">
        <citations>
            <citation type="doi">10.1093/nar/gkq1019</citation>
            <citation type="bibtex">
@misc{github_sratools,