Mercurial > repos > cpt > cpt_req_phage_start

comparison gff3_require_phage_start.xml @ 4:5de686a70681 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:52:41 +0000
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3:67e5202e43c9 4:5de686a70681
1 <tool id="edu.tamu.cpt.gff3.require_phage_start" name="GFF3 Filter: Require Phage Start" version="19.1.0.0">
2 <description>ensures start is ATG, TTG, or GTG</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 '$__tool_directory__/gff3_require_phage_start.py'
12
13 @GENOME_SELECTOR@
14 '$gff3_data'
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 start codon"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="reference_genome_source" value="history"/>
29 <param name="genome_fasta" value="T7_ReqPhageIn.fasta"/>
30 <param name="gff3_data" value="T7_ReqPhageIn.gff3"/>
31 <output name="stdout" file="T7_ReqPhageOut.gff3"/>
32 </test>
33 <test>
34 <param name="reference_genome_source" value="history"/>
35 <param name="genome_fasta" value="Miro_ReqPhageIn.fa"/>
36 <param name="gff3_data" value="Miro_ReqPhageIn.gff3"/>
37 <output name="stdout" file="Miro_ReqPhageOut.gff3"/>
38 </test>
39 </tests>
40 <help><![CDATA[
41 **What it does**
42
43 Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.
44
45 .. class:: warningmark
46
47 The tool only retains *gene* and *CDS* features that pass this filter.
48 ]]></help>
49 <expand macro="citations"/>
50 </tool>