<tool id="cg_testvariants" name="TestVariants" version="1.7.1.b">
    <description>Test for the presence of variants</description> 

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

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

    <command>
        cgatools testvariants
        --beta
        --reference

            #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
        --input $listing
        --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="Genome reference (in complete genomics CRR format)" help="Some indexes are available at ftp://ftp.completegenomics.com/ReferenceFiles/">
                <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>

        <!--form fields to select variant list-->
        <param name="listing" type="data" format="tabular" label="Select variant list"/>

        <!--conditional to select input file type-->
        <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">
                    <param name="input" type="data" format="cg_var" label="Dataset"/>
                </repeat>
            </when>
            <when value="mastervar">						
                <repeat name="varfiles" title="Variant files">
                    <param name="input" type="data" format="cg_mastervar" label="Dataset"/>				
                </repeat>
            </when>
        </conditional>

        <!-- prefix for output file so you dont have to manually rename history items -->
        <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 testvariants to test variant or mastervar files for the presence of variants.

**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
          testvariants - Tests variant files for presence of variants.
        
        DESCRIPTION
          Tests variant files for presence of variants. The output is a tab-delimited
          file consisting of the columns of the input variants file, plus a column 
          for each assembly results file that contains a character code for each 
          allele. The character codes have meaning as follows:
            
            0 This allele of this genome is consistent with the reference at this 
              locus but inconsistent with the variant.
            1 This allele of this genome has the input variant at this locus.
            N This allele of this genome has no-calls but is consistent with the 
              input variant.
        
        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.
        
          --input arg (=STDIN)
              The input variants to test for.
        
          --output arg (=STDOUT)
              The output file (may be omitted for stdout).
        
          --variants arg
              The input variant files (may be passed in as arguments at the end of 
              the command).
        
        SUPPORTED FORMAT_VERSION
          0.3 or later
    </help>
</tool>