Mercurial > repos > cpt > cpt_wig_rebase

comparison wig_rebase.xml @ 2:ae5f291c788d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:54:16 +0000
parents
children 4451729a0a3b
comparison
equal deleted inserted replaced
1:143624dee31b 2:ae5f291c788d
1 <tool id="edu.tamu.cpt.wig.rebase" name="Rebase Wig Analysis Results" version="19.1.0.0">
2 <description>against parent features</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 python '$__tool_directory__/wig_rebase.py'
10 '$parent'
11 '$wigFile'
12
13 '$protein2dna'
14 --map_by "$map_by"
15 > '$output']]></command>
16 <inputs>
17 <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
18 <param label="Wig Results" name="wigFile" format="wig" type="data"/>
19 <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
20 <param label="Mapping Key" name="map_by" type="text" value="ID"/>
21 </inputs>
22 <outputs>
23 <data format="wig" name="output"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="parent" value="T7_CLEAN.gff3"/>
28 <param name="wigFile" value="T7_BW_I.wig"/>
29 <param name="protein2dna" value="--protein2dna"/>
30 <param name="map_by" value="ID"/>
31 <output name="output" file="T7_BW_I_REBASE.wig"/>
32 </test>
33 <test>
34 <param name="parent" value="tmhmm.parent.gff3"/>
35 <param name="wigFile" value="tmhmm_m.wig"/>
36 <param name="protein2dna" value="--protein2dna"/>
37 <param name="map_by" value="ID"/>
38 <output name="output" file="rebased_m.wig"/>
39 </test>
40 </tests>
41 <help><![CDATA[
42 **What it does**
43
44 Rebases wig results against a set of gff3 annotations which were involved in producing that data.
45
46 For example, imagine you take a gff3 file, and export the CDS sequences in
47 order to analyse in TMHMM. Having done this, you want to view the associated
48 Wig files in JBrowse with your TMHMM results. This tool will re-map the wig
49 data to the correct location in the parent genome.
50
51 E.g. Given
52
53 - A feature (gp01) runs from 2000-2200
54 - A wig file with data from 1-200
55
56 The data would be re-mapped and you would receive a wig file with data from 2000-2200.
57 ]]></help>
58 <expand macro="citations"/>
59 </tool>