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view diversity_pi.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents
children 8997f2ca8c7a
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<tool id="gd_diversity_pi" name="Diversity" version="1.0.0">
  <description>&amp;pi;</description>

  <command interpreter="python">
    diversity_pi.py "$input" "$coverage_input" "$indiv_input" "$min_coverage" "$output"
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
        #set $arg = '%s:%s' % ($individual_col, $individual)
        "$arg"
    #end for
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />
    <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
    <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
  </inputs>

  <outputs>
    <data name="output" format="txt" metadata_source="input" />
  </outputs>

  <help>
  </help>
</tool>