Mercurial > repos > cpt > cpt_require_shine

comparison cpt_req_sd/gff3_require_sd.xml @ 0:ae2791f3108f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author cpt
date Fri, 13 May 2022 05:35:34 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:ae2791f3108f
1 <tool id="edu.tamu.cpt.gff3.require_sd" name="Gff3 Filter: Require SD" version="19.1.0.0">
2 <description>ensures CDSs have an SD</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 @GENOME_SELECTOR_PRE@
10
11 python $__tool_directory__/gff3_require_sd.py
12
13 @GENOME_SELECTOR@
14 @INPUT_GFF@
15
16 > $stdout
17
18 ]]></command>
19 <inputs>
20 <expand macro="genome_selector" />
21 <expand macro="gff3_input" />
22 </inputs>
23 <outputs>
24 <data format="gff3" name="stdout" label="$gff3_data.name filtered for SD presence"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="reference_genome_source" value="history" />
29 <param name="genome_fasta" value="T7_ReqSDIn.fasta" />
30 <param name="gff3_data" value="T7_ReqSDIn.gff3" />
31
32 <output name="stdout" file="T7_ReqSDOut.gff3" />
33 </test>
34 <test>
35 <param name="reference_genome_source" value="history" />
36 <param name="genome_fasta" value="Miro_ReqSDIn.fa" />
37 <param name="gff3_data" value="Miro_ReqSDIn.gff3" />
38
39 <output name="stdout" file="Miro_ReqSDOut.gff3" />
40 </test>
41 </tests>
42 <help><![CDATA[
43 **What it does**
44
45 Ensures every CDS has an upstream Shine-Dalgarno site defined. ShineFind is used to add SD subfeatures to CDSs without one.
46
47 .. class:: warningmark
48
49 This tool removes non-CDS type features, and CDS features without an SD site (RBS features are ignored).
50
51 ]]></help>
52 <expand macro="citations" />
53 </tool>