annotate select_individuals.xml @ 4:7a94f11fe71f

change output.extra_files_path to output.files_path

<tool id="gd_select_individuals" name="Select" version="1.0.0">
  <description>individuals from a SNP table</description>

  <command interpreter="bash">
    echo.bash "$input" "$output"
    #for $individual in str($individuals).split(',')
        #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
        #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
        #set $arg = '\t'.join([$individual_col, $individual, ''])
        "$arg"
    #end for
  </command>

  <inputs>
    <param name="input" type="data" format="wsf"/>
    <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
      <options>
        <filter type="data_meta" ref="input" key="individual_names" />
      </options>
      <validator type="no_options" message="You must select at least one individual"/>
    </param>
  </inputs>

  <outputs>
    <data name="output" format="ind" label="Individuals from ${input.hid}" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.wsf" ftype="wsf" />
      <param name="individuals" value="PB1,PB2" />
      <output name="output" file="test_in/a.ind" />
    </test>
  </tests>

  <help>
**What it does**

The user selects a SNP table and a set of individuals from the table.
The command saves that list of individuals for use by other Galaxy tools.
  </help>
</tool>