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comparison cpt_fix_sixpack/gff3_fix_sixpack.xml @ 0:b3ed429dd8ab draft

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author cpt
date Fri, 13 May 2022 18:01:18 +0000
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1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
3 <description>Properly formats naive ORF caller output for Apollo</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[
10 $__tool_directory__/gff3_fix_sixpack.py
11 @INPUT_GFF@
12 > $output]]></command>
13 <inputs>
14 <expand macro="gff3_input" />
15 </inputs>
16 <outputs>
17 <data format="gff3" name="output"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="gff3_data" value="miro.gff3" />
22 <output name="output" file="miro.6pfix.gff3" />
23 </test>
24 <test>
25 <param name="gff3_data" value="miro.cds.gff3" />
26 <output name="output" file="miro.cds6pfix.gff3" />
27 </test>
28 </tests>
29 <help><![CDATA[
30 **What it does**
31
32 This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats
33 the output of the naïve ORF call Sixpack such that it will be compatible with
34 Apollo via JBrowse.
35
36 ]]></help>
37 <expand macro="citations" />
38 </tool>