Mercurial > repos > cpt > cpt_intersect_adjacent
comparison cpt_intersect_adj/intersect_and_adjacent.xml @ 0:4c72b6accdee draft
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author | cpt |
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date | Fri, 13 May 2022 05:05:59 +0000 |
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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> |