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comparison cpt_promote_qualifiers/promote_qualifier.xml @ 0:6f4c46313117 draft default tip

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author cpt
date Fri, 17 Jun 2022 13:05:11 +0000
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1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt.gff3.promote_qualifiers" name="Promote Qualifers" version="20.0.0">
3 <description>Promote a child feature's qualifier into the parent feature</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[
10 python $__tool_directory__/promote_qualifier.py
11 @INPUT_GFF@
12 $parent
13 $child
14 $qualifier
15 > $output]]></command>
16 <inputs>
17 <expand macro="gff3_input" />
18 <param label="Parent Feature Type" name="parent" type="text" help="e.g. gene, mRNA, exon" />
19 <param label="Child Feature Type" name="child" type="text" help="e.g. mRNA, exon, CDS" />
20 <param label="Qualifer to Promote" name="qualifier" type="text" help="e.g. Name, Product, Notes" />
21 </inputs>
22 <outputs>
23 <data format="gff3" name="output" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="gff3_data" value="promote_qualifiers_in.gff3" />
28 <param name="parent" value="gene" />
29 <param name="child" value="mRNA" />
30 <param name="qualifier" value="Name" />
31 <output name="output" file="promote_qualifiers_out.gff3" />
32 </test>
33 </tests>
34 <help><![CDATA[
35 **What it does**
36
37 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.
38
39 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):
40
41 *Before*::
42
43 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
44 NC_049846.1 . mRNA 630 1182 . + . Parent=8942304a;ID=536ddf54; Name=Gene_1_Name ;date_creation=2020-09-25
45
46 *After*::
47
48 NC_049846.1 . gene 630 1182 . + . ID=8942304a;date_last_modified=2020-09-25; Name=Gene_1_Name ;date_creation=2020-09-25
49 NC_049846.1 . mRNA 630 1182 . + . Parent=8942304a;ID=536ddf54; Name=Gene_1_Name ;date_creation=2020-09-25
50
51 .. class:: infomark
52
53 **Notes**::
54
55 - If the qualifier is already present in the parent, it will be overwritten with the child's value.
56 - 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.
57 - For positive strand features it will select the child with the smaller start coordinate.
58 - For negative strand it will select the child with the largest end coordinate.
59
60 .. class:: warningmark
61
62 **Warning**::
63
64 You should likely never run this to promote the "ID" qualifier as this will break the gff3 hierarchy structure and cause parsing failures downstream.
65 ]]></help>
66 <expand macro="citations-clm" />
67 </tool>