|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool id="edu.tamu.cpt.gff3.intersect_and_adjacent" name="Intersect and Adjacent" version="21.0.0">
|
|
|
3 <description>Outputs nearby top-level GFF features from two GFF3 files</description>
|
|
|
4 <macros>
|
|
|
5 <import>macros.xml</import>
|
|
|
6 <import>cpt-macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <requirements>
|
|
|
9 <requirement type="package" version="3.7">python</requirement>
|
|
|
10 <requirement type="package" version="1.79">biopython</requirement>
|
|
|
11 <requirement type="package" version="1.1.3">cpt_gffparser</requirement>
|
|
|
12 <requirement type="package" version="3.0.2">intervaltree</requirement>
|
|
|
13 </requirements>
|
|
|
14 <command detect_errors="aggressive"><![CDATA[
|
|
|
15 $__tool_directory__/intersect_and_adjacent.py
|
|
|
16 "$gff3_data_a"
|
|
|
17 "$gff3_data_b"
|
|
|
18 $window
|
|
|
19 $stranding
|
|
|
20 --oa $oa
|
|
|
21 --ob $ob
|
|
|
22 ]]></command>
|
|
|
23 <inputs>
|
|
|
24 <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/>
|
|
|
25 <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/>
|
|
|
26 <param label="Adjacency Window Size" name="window" type="integer" value = "0"/>
|
|
|
27 <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue="" />
|
|
|
28 </inputs>
|
|
|
29 <outputs>
|
|
|
30 <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/>
|
|
|
31 <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/>
|
|
|
32 </outputs>
|
|
|
33 <tests>
|
|
|
34 <test>
|
|
|
35 <param name="gff3_data_a" value="T7_IntersectAIn.gff3" />
|
|
|
36 <param name="gff3_data_b" value="T7_IntersectBIn.gff3" />
|
|
|
37 <param name="window" value= "50" />
|
|
|
38 <param name="stranding" value= "-stranding"/>
|
|
|
39 <output name="oa" file="T7_IntersectAOut.gff3"/>
|
|
|
40 <output name="ob" file="T7_IntersectBOut.gff3"/>
|
|
|
41 </test>
|
|
|
42 </tests>
|
|
|
43 <help><![CDATA[
|
|
|
44 **What it does**
|
|
|
45
|
|
|
46 Given two input files, this tool computes the members of A that are within
|
|
|
47 "Window" nucleotides of a member of B, and vice versa. It then produces
|
|
|
48 two gff3 outputs, one being the features of GFF A that pass this check,
|
|
|
49 and the other being the features of GFF B that pass.
|
|
|
50 ]]></help>
|
|
|
51 <expand macro="citations-2020" />
|
|
|
52 </tool>
|
