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comparison cpt_req_phage_start/gff3_require_phage_start.xml @ 0:45a5cf6b0ff4 draft

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author cpt
date Fri, 13 May 2022 05:31:56 +0000
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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
32 <output name="stdout" file="T7_ReqPhageOut.gff3" />
33 </test>
34 <test>
35 <param name="reference_genome_source" value="history" />
36 <param name="genome_fasta" value="Miro_ReqPhageIn.fa" />
37 <param name="gff3_data" value="Miro_ReqPhageIn.gff3" />
38
39 <output name="stdout" file="Miro_ReqPhageOut.gff3" />
40 </test>
41 </tests>
42 <help><![CDATA[
43 **What it does**
44
45 Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.
46
47 .. class:: warningmark
48
49 The tool only retains *gene* and *CDS* features that pass this filter.
50 ]]></help>
51 <expand macro="citations" />
52 </tool>