view cpt_gff_add_parent/gff3_add_parents_to_cds.xml @ 0:60651e90119a draft

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<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff3.cdsParents" name="GFF3 Add Gene to CDS" version="19.1.0.0">
  <description>is one step of fixing a gene model--adding parent gene features to CDSs</description>
  <macros>
    <import>macros.xml</import>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
$__tool_directory__/gff3_add_parents_to_cds.py
@INPUT_GFF@
> $output]]></command>
  <inputs>
      <expand macro="gff3_input" />
  </inputs>
  <outputs>
    <data format="gff3" name="output"/>
  </outputs>
  <tests>
                <test>
			<param name="gff3_data" value="T7_AddParentIn.gff3" />
			<output name="output">
                          <assert_contents>
			    <has_line line="##gff-version 3"/>
			    <has_n_lines n="10105" />
			  </assert_contents>
			</output>
		</test>
		<test>
			<param name="gff3_data" value="Miro_AddParentIn.gff3" />
			<output name="output">
                          <assert_contents>
			    <has_line line="##gff-version 3"/>
			    <has_n_lines n="829" />
			  </assert_contents>
			</output>
		</test>
  </tests>
  <help><![CDATA[
**What it does**

This tool updates the gene model in a GFF3, useful when a nonstandard gene model 
has been applied. It finds all CDS features, **strips their parent features**, 
then applies a gene-mRNA-CDS model, compliant with the standard GFF3 format.

Warning: Use this tool only when it is absolutely necessary to fix a gene model. 

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