<tool id="edu.tamu.cpt.gff3.filter_type" name="GFF3 Feature Type Filter" version="19.1.0.0">
  <description>selects features from a gff3 file based on feature type</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
#set repeat_data = '" "'.join([ str($var.type) for $var in $repeat_0 ])

'python $__tool_directory__/filter_type.py'
@INPUT_GFF@
"$repeat_data"
'$invert'
> '$output']]></command>
  <inputs>
    <expand macro="gff3_input"/>
    <repeat name="repeat_0" title="Feature Types">
      <param label="Feature type" name="type" type="text"/>
    </repeat>
    <param checked="true" label="Invert the filter" name="invert" type="boolean" truevalue="--invert" falsevalue=""/>
  </inputs>
  <outputs>
    <data format="gff3" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="gff3_data" value="Miro_FilterIn.gff3"/>
      <param name="repeat_0_0|type" value="CDS"/>
      <param name="invert" value="False"/>
      <output name="output" file="Miro_FilterOut1.gff3"/>
    </test>
    <test>
      <param name="gff3_data" value="Miro_FilterIn.gff3"/>
      <param name="repeat_0_0|type" value="CDS"/>
      <param name="invert" value="--invert"/>
      <output name="output" file="Miro_FilterOut2.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

The tool finds the specified feature type(s) in an input GFF3 and will output 
**only** the specified feature type. By selecting the inversion, **everything except** 
the specified feature type(s) will be included in the output GFF3.

For example, user may output **only** ``Shine_Dalgarno_sequence`` type features, or,
inverting that, output everything but ``Shine_Dalgarno_sequence`` type features. Any 
feature type used in the input GFF3 can be filtered; typical options would include gene, 
mRNA, CDS, tRNA, and terminator. The input name format must follow sequence ontology 
convention (http://www.sequenceontology.org/).

      ]]></help>
  <expand macro="citations"/>
</tool>