annotate gemini_macros.xml @ 4:ba3abde6775b draft default tip

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<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.10.0">gemini</requirement>
            <requirement type="package" version="0.1.3">grabix</requirement>
            <requirement type="package" version="0.2.6">tabix</requirement>
            <requirement type="package" version="0.1.19">samtools</requirement>
            <requirement type="package" version="2.19.1">bedtools</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>gemini --version</version_command>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <xml name="annotation_dir">
        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
            <options from_data_table="gemini_databases">
                <filter type="sort_by" column="0" />
                <validator type="no_options" message="No annotation database is available" />
            </options>
        </param>
    </xml>

    <xml name="add_header_column">
        <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" 
            label="Add a header of column names to the output" help="(--header)"/>
    </xml>

    <xml name="radius">
        <param name="radius" type="integer" value="3" size="5" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
            <validator type="in_range" min="0"/>
        </param>
    </xml>
    <xml name="variant_mode">
        <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" 
            label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
    </xml>

    <xml name="column_filter">
        <conditional name="report">
            <param name="report_selector" type="select" label="Columns to include in the report"
                help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
                <option value="all" selected="True">all</option>
                <option value="column_filter">User given columns</option>
            </param>
            <when value="all"/>
            <when value="column_filter">
                <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
                    <option value="gene">gene</option>
                    <option value="chrom">chrom</option>
                    <option value="start">start</option>
                    <option value="end">end</option>
                    <option value="ref">ref</option>
                    <option value="alt">alt</option>
                    <option value="impact">impact</option>
                    <option value="impact_severity">impact_severity</option>
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="filter">
        <conditional name="filter">
            <param name="filter_selector" type="select" label="Apply additional constraints"
                help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.">
                <option value="no">No additional constraints</option>
                <option value="yes">Apply additional constraints</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="filter" type="text" size="20" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)">
                    <expand macro="sanitize_query" />
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="sanitize_query">
        <sanitizer invalid_char="">
            <valid initial="string.printable"/>
       </sanitizer>
    </xml>

    <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="min_sequence_depth">
        <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample"
                help="default: 0 (-d)">
            <validator type="in_range" min="0"/>
        </param>
    </xml>

    <token name="@VERSION@">0.10.1</token>

    <token name="@CITATION@">------

**Citation**

If you use GEMINI in your research, please cite the following manuscript:

  </token>
  <xml name="citations">
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
        <yield />
    </citations>
  </xml>

    <xml name="infile">
        <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
            <options options_filter_attribute="metadata.gemini_version" >
                <filter type="add_value" value="@VERSION@" />
            </options>
            <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>
        </param>
    </xml>

</macros>