view listvariants.xml @ 1:fec197eb2f00 draft

Uploaded

<tool id="cga_listvariant" name="listvariants" version="0.0.1">

  <description>lists all called variants</description> <!--adds description in toolbar-->
  
  <command> <!--run executable-->
    cgatools listvariants
      --beta
      --reference ${crr.fields.path}
      --output $output
      --variants 
      #for $v in $varfiles <!--get each var file-->
      ${v.input}
      #end for
      #if $include_list.listing == "yes" <!--only added when yes-->
        --variant-listing $include_list.list
      #end if
      $longvar
  </command>

  <inputs>
  	<!--form field to select crr file-->
    <param name="crr" type="select" label="Genome build">
      <options from_data_table="cgatools" />
    </param>

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

  	<!--form fields to include existing variant list-->
    <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>

  	<!--form field to select all variant files-->
    <repeat name="varfiles" title="Var file">
      <param name="input" type="data" format="tabular" label="Dataset">
        <validator type="unspecified_build" />
        <validator type="dataset_metadata_in_file" filename="cgatools.loc"
         metadata_name="dbkey" metadata_column="0"
         message="cgatools is not currently available for this build."/>
      </param>
    </repeat>
  </inputs>
  
  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <help>

**What it does**

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

cgatools: http://sourceforge.net/projects/cgatools/files/

-----

**cgatools Manual**::

		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>