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comparison gff3_fix_sixpack.xml @ 3:efa4dfc23549 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:28 +0000
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2:6a9b026cb378 3:efa4dfc23549
1 <tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
2 <description>Properly formats naive ORF caller output for Apollo</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 '$__tool_directory__/gff3_fix_sixpack.py'
10 @INPUT_GFF@
11 > '$output']]></command>
12 <inputs>
13 <expand macro="gff3_input"/>
14 </inputs>
15 <outputs>
16 <data format="gff3" name="output"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="gff3_data" value="miro.gff3"/>
21 <output name="output" file="miro.6pfix.gff3"/>
22 </test>
23 <test>
24 <param name="gff3_data" value="miro.cds.gff3"/>
25 <output name="output" file="miro.cds6pfix.gff3"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 **What it does**
30
31 This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats
32 the output of the naïve ORF call Sixpack such that it will be compatible with
33 Apollo via JBrowse.
34
35 ]]></help>
36 <expand macro="citations"/>
37 </tool>