<tool id="cg_listvariant" name="ListVariants" version="1.7.1">

    <description>Lists all variants present in CG var or masterVar file</description> 

    <requirements>
        <requirement type="package" version="1">cgatools17</requirement>
    </requirements>

    <version_command>cgatools | head -1</version_command>

    <command> <!--run executable-->
        cgatools
            listvariants
            --beta

            #if $reference_gene_sets_source.source_select == "indexed_filtered"
                ${reference_gene_sets_source.crr.fields.crr_path}
            #else if $reference_gene_sets_source.source_select == "history"
                ${reference_gene_sets_source.crr}
            #end if
            
            --output $output
            #if $include_list.listing == "yes" <!--only added when yes-->
                --variant-listing $include_list.list
            #end if
            $longvar
            --variants 
            #for $v in $file_types.varfiles <!--get each var/mastervar file-->
                    ${v.input}
            #end for

    </command>

    <inputs>
    <!--form field to select crr file-->
        <conditional name="reference_gene_sets_source">
            <param name="source_select" type="select" label="GFF/GTF Source">
                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
                <option value="history">Use reference from the history</option>
            </param>
            <when value="indexed_filtered">
                <param name="crr" type="select" label="Reference Build">
                    <options from_data_table="cg_anno_files" />
                </param>
            </when>
                <when value="history">
                    <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
                </when>
        </conditional>

        <conditional name="file_types">
            <param name="file_type" type="select" label="Select the input file type">
                <option value="var" selected="true">var files</option>
                <option value="mastervar">mastervar files</option>
            </param>
            <when value="var">
                <repeat name="varfiles" title="Variant files" min="1">
                    <param name="input" type="data" format="cg_var" label="Dataset"/>
                </repeat>
            </when>
            <when value="mastervar">
                <repeat name="varfiles" title="Variant files" min="1">
                    <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
                </repeat>					
            </when>
        </conditional>

        <param name="longvar" type="select" label="List long variants?">
            <option value="" selected="true">no</option>
            <option value="--list-long-variants">yes</option>
        </param>

        <conditional name="include_list">
            <param name="listing" type="select" label="Include variant listing?">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="list" type="data" format="tabular" label="Variant listing"/>
            </when>
        </conditional>
        <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>		
    </inputs>
  
    <outputs>
        <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
    </outputs>

    <help>
**What it does**

This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.

**cgatools 1.7.1 Documentation**

Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf

Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf

**Command line reference**::

        COMMAND NAME
          listvariants - Lists the variants present in a variant file.

        DESCRIPTION
          Lists all called variants present in the specified variant files, in a 
          format suitable for processing by the testvariants command. The output is a
          tab-delimited file consisting of the following columns:
             
            variantId  Sequential id assigned to each variant.
            chromosome The chromosome of the variant.
            begin      0-based reference offset of the beginning of the variant.
            end        0-based reference offset of the end of the variant.
            varType    The varType as extracted from the variant file.
            reference  The reference sequence.
            alleleSeq  The variant allele sequence as extracted from the variant 
                       file.
            xRef       The xRef as extrated from the variant file.

        OPTIONS
          -h [ --help ] 
              Print this help message.

          --beta 
              This is a beta command. To run this command, you must pass the --beta 
              flag.

          --reference arg
              The reference crr file.

          --output arg (=STDOUT)
              The output file (may be omitted for stdout).

          --variants arg
              The input variant files (may be positional args).

          --variant-listing arg
              The output of another listvariants run, to be merged in to produce the 
              output of this run.

          --list-long-variants 
              In addition to listing short variants, list longer variants as well 
              (10's of bases) by concatenating nearby calls.

        SUPPORTED FORMAT_VERSION
          0.3 or later
    </help>
</tool>