<tool id="gff_filter_by_feature_count" name="Filter GFF data by feature count" version="0.1">

  <description>using simple expressions</description>

  <command interpreter="python">

    gff_filter_by_feature_count.py $input_file1 $out_file1 "$feature_name" "$cond"

  </command>

  <inputs>

    <param format="gff" name="input_file1" type="data" label="Filter"/>

    <param name="feature_name" type="select" label="Using feature name">

        <options from_dataset="input_file1">

            <column name="name" index="2"/>

            <column name="value" index="2"/>

            <filter type="unique_value" name="unique" column="2"/>

        </options>

    </param>

    <param name="cond" size="40" type="text" value=">0" label="With following condition">

      <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/>

    </param>

  </inputs>

  <outputs>

    <data format="input" name="out_file1" metadata_source="input_file1"/>

  </outputs>

  <tests>

      <!-- Test GTF filtering. -->

      <test>

          <param name="input_file1" value="gops_subtract_in1.gff"/>

          <param name="feature_name" value="exon"/>

          <param name="cond" value=">1"/>

          <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/>

      </test>

      <!-- Test GFF3 filtering. -->

      <test>

          <param name="input_file1" value="5.gff3"/>

          <param name="feature_name" value="HSP"/>

          <param name="cond" value=">=5"/>

          <output name="out_file1" file="gff_filter_by_feature_count_out2.gff"/>

      </test>

  </tests>



  <help>





.. class:: infomark



Valid comparison operators are: &gt; &lt; &gt;=, &lt;=, !=, and ==



-----



**Syntax**



The filter tool allows you to restrict the dataset based on transcripts' feature counts.



</help>

</tool>