<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff3.promote_qualifiers" name="Promote Qualifers" version="20.0.0">
  <description>Promote a child feature's qualifier into the parent feature</description>
  <macros>
    <import>macros.xml</import>
	<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/promote_qualifier.py
@INPUT_GFF@
$parent
$child
$qualifier
> $output]]></command>
  <inputs>
    <expand macro="gff3_input" />
    <param label="Parent Feature Type" name="parent" type="text" help="e.g. gene, mRNA, exon" />
    <param label="Child Feature Type" name="child" type="text" help="e.g. mRNA, exon, CDS" />
    <param label="Qualifer to Promote" name="qualifier" type="text" help="e.g. Name, Product, Notes" />
  </inputs>
  <outputs>
    <data format="gff3" name="output" />
  </outputs>
  <tests>
      <test>
          <param name="gff3_data" value="promote_qualifiers_in.gff3" />
          <param name="parent" value="gene" />
          <param name="child" value="mRNA" />
          <param name="qualifier" value="Name" />
          <output name="output" file="promote_qualifiers_out.gff3" />
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Allows you to copy a specified qualifier value from a child feature into a parent feature, most likely to copy the Name from an mRNA into a gene. 

For example, for a *Parent Feature Type* of "gene", *Child Feature Type* of "mRNA", and *Qualifier to Promote* of "Name" the following gff will be changed (spacing for emphasis):

*Before*::

  NC_049846.1	.	gene	630	1182	.	+	.	ID=8942304a;date_last_modified=2020-09-25;   Name=NC_049846.1.gene_1   ;date_creation=2020-09-25
  NC_049846.1	.	mRNA	630	1182	.	+	.	Parent=8942304a;ID=536ddf54;   Name=Gene_1_Name   ;date_creation=2020-09-25

*After*::

  NC_049846.1	.	gene	630	1182	.	+	.	ID=8942304a;date_last_modified=2020-09-25;   Name=Gene_1_Name   ;date_creation=2020-09-25
  NC_049846.1	.	mRNA	630	1182	.	+	.	Parent=8942304a;ID=536ddf54;   Name=Gene_1_Name   ;date_creation=2020-09-25

.. class:: infomark 

**Notes**::

  - If the qualifier is already present in the parent, it will be overwritten with the child's value. 
  - If there are multiple child features of the specified type under the same parent, the value from the first child. This action is strand aware. 
    - For positive strand features it will select the child with the smaller start coordinate. 
    - For negative strand it will select the child with the largest end coordinate.

.. class:: warningmark 

**Warning**::

  You should likely never run this to promote the "ID" qualifier as this will break the gff3 hierarchy structure and cause parsing failures downstream. 
]]></help>
		<expand macro="citations-clm" />
</tool>