view summarize_gff_by_attribute.xml @ 12:755a4d643184 draft default tip

planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23

<tool id="summarize_gff_by_attribute" name="Create summary on GFF3 attribute" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package">bioconductor-rtracklayer</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="summarize_gff_by_attribute.R"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript  $__tool_directory__/summarize_gff_by_attribute.R '$input_gff' $attribute_name '$output_table'
    ]]></command>
    <inputs>
      <param type="data" name="input_gff" format="gff" label="Input GFF">
        <sanitizer invalid_char="">
          <valid initial="string.ascii_letters,string.digits">
            <add value="_" />
          </valid>
        </sanitizer>
      </param>
        <param type="text" name="attribute_name" label="Name of attribute to summarize" optional="false" default="Name"/>
    </inputs>
    <outputs>
        <data name="output_table" format="tsv" />
    </outputs>
    <help><![CDATA[
        Calculate summary statistics on GFF3 attribute. Summary included total number of features and total lenght per attribute value.
    ]]></help>
</tool>