comparison gemini_macros.xml @ 2:9ed33f571d1d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

1:5fd4a5f9ee31

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.18.1">gemini</requirement>
            <requirement type="package" version="0.2.6">tabix</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">

                    <option value="alt">alt</option>
                    <option value="impact">impact</option>
                    <option value="impact_severity">impact_severity</option>
                    <option value="max_aaf_all">alternative allele frequency</option>
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="filter">

    <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
        #if str($filter.filter_selector) == 'yes' and $filter.filter:
            #import pipes
            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
        #end if
    </token>

    <xml name="family">
        <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>

2:9ed33f571d1d

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.18.1">gemini</requirement>
            <requirement type="package" version="0.2.6">tabix</requirement>
            <!-- for conda useage -->
            <!--requirement type="package" version="1.3.1">htslib</requirement-->
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">

                    <option value="alt">alt</option>
                    <option value="impact">impact</option>
                    <option value="impact_severity">impact_severity</option>
                    <option value="max_aaf_all">alternative allele frequency</option>
                </param>
                <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
            </when>
        </conditional>
    </xml>

    <xml name="filter">

    <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
        #if str($filter.filter_selector) == 'yes' and $filter.filter:
            #import pipes
            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
        #end if
    </token>

    <token name="@COLUMN_SELECT@">
        #if $report.report_selector != 'all':
            --columns "${report.columns}
            #if str($report.extra_cols).strip()
                #echo ','+','.join(str($report.extra_cols).split()) 
            #end if
            "
        #end if
    </token>

    <xml name="family">
        <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>