annotate gemini_autosomal_recessive.xml @ 4:05124dc72dba draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

<tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.1">
    <description>Find variants meeting an autosomal recessive/dominant model</description>
    <macros>
        <import>gemini_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini

            #if str($rec_or_dom) == 'recessive':
                ## start autosomal_recessive
                autosomal_recessive
            #else:
                ## start autosomal_dominant
                autosomal_dominant
            #end if

            @COLUMN_SELECT@

            @CMDLN_SQL_FILTER_FILTER_OPTION@

            -d $d
            #if int($min_kindreds) > 0:
                --min-kindreds $min_kindreds
            #end if

            #if str($families).strip():
                --families "$families"
            #end if

            $lenient
            $allow_unaffected

            #if int($min_gq) > 0:
                --min-gq $min_gq
            #end if

            #if int($gt_pl_max) > -1:
                --gt-pl-max $gt_pl_max
            #end if

            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <inputs>

        <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
            <option value="recessive">recessive</option>
            <option value="dominant">dominant</option>
        </param>

        <expand macro="infile" />
        <expand macro="column_filter" />
        <expand macro="filter" />
        <expand macro="min_sequence_depth" />
        <expand macro="family" />
        <expand macro="lenient" />
        <expand macro="unaffected" />
        <expand macro="min_kindreds" />
        <expand macro="min_gq" />
        <expand macro="gt_pl_max" />

    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
            <param name="rec_or_dom" value="dominant" />
            <conditional name="report">
                <param name="report_selector" value="column_filter" />
                <param name="columns" value="gene,chrom,impact" />
            </conditional>
            <param name="lenient" value="true" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="infile" value="gemini_auto_rec_input.db" ftype="gemini.sqlite" />
            <param name="rec_or_dom" value="recessive" />
            <conditional name="report">
                <param name="report_selector" value="column_filter" />
                <param name="columns" value="gene,chrom,impact" />
            </conditional>
            <param name="lenient" value="true" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**

Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a
built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern.
The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts.

    </help>
    <expand macro="citations"/>
</tool>