annotate draw_variants.xml @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

<tool id="gd_draw_variants" name="Draw" version="1.0.0">
  <description>variants</description>

  <command interpreter="python">
    #import json
    #import base64
    #import zlib
    #set $ind_names = $input.dataset.metadata.individual_names
    #set $ind_colms = $input.dataset.metadata.individual_columns
    #set $ind_dict = dict(zip($ind_names, $ind_colms))
    #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
    #set $ind_comp = zlib.compress($ind_json, 9)
    #set $ind_arg = base64.b64encode($ind_comp)
    draw_variants.py '$input' '$indel_input' '$coverage_input' '$annotation_input' '$indiv_input' '$ref_name' '$min_coverage' '$output' '$ind_arg'
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <param name="indel_input" type="data" format="gd_snp" label="Indel dataset" />
    <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />
    <param name="annotation_input" type="data" format="interval" label="Annotation dataset" />
    <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />

    <param name="ref_name" type="select" label="Ref name">
      <options from_dataset="indiv_input">
        <column name="name" index="1"/>
        <column name="value" index="1"/>
        <filter type="add_value" name="default" value="default" index="0" />
      </options>
    </param>

    <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
  </inputs>

  <outputs>
    <data name="output" format="svg" />
  </outputs>

  <help>
  </help>
</tool>