comparison gff2gb.xml @ 3:c8fcb7246ac3 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:44:32 +0000
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2:6795d3349462 3:c8fcb7246ac3
1 <tool id="edu.tamu.cpt.gff.gff2gb" name="GFF3 to GenBank" version="4.0">
2 <description>convert gff3 to GenBank</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 $__tool_directory__/gff2gb.py'
12 @INPUT_GFF@
13 @INPUT_FASTA@
14 --transltbl '$transltbl'
15 > '$output']]></command>
16 <inputs>
17 <expand macro="input/gff3+fasta"/>
18 <param label="Translation Table" name="transltbl" type="select">
19 <option value="1">1. The Standard Code</option>
20 <option value="2">2. The Vertebrate Mitochondrial Code</option>
21 <option value="3">3. The Yeast Mitochondrial Code</option>
22 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
23 <option value="5">5. The Invertebrate Mitochondrial Code</option>
24 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
25 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
26 <option value="10">10. The Euplotid Nuclear Code</option>
27 <option value="11" selected="true">11. The Bacterial, Archaeal and Plant Plastid Code</option>
28 <option value="12">12. The Alternative Yeast Nuclear Code</option>
29 <option value="13">13. The Ascidian Mitochondrial Code</option>
30 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
31 <option value="16">16. Chlorophycean Mitochondrial Code</option>
32 <option value="21">21. Trematode Mitochondrial Code</option>
33 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
34 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
35 <option value="24">24. Pterobranchia Mitochondrial Code</option>
36 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
37 </param>
38 </inputs>
39 <outputs>
40 <data format="genbank" hidden="false" name="output" label="${gff3_data.name} as GenBank"/>
41 </outputs>
42 <tests>
43 <!-- There have been issues running the diffs for the files -->
44 <!-- Going to use asserts and run ONE (or no) diffs -->
45 <test>
46 <!-- ORIGINAL TEST FILE, regenerated 10.12.2020 -->
47 <param name="reference_genome_source" value="history"/>
48 <param name="genome_fasta" value="miro.fa"/>
49 <param name="gff3_data" value="miro.gff3"/>
50 <output name="output" file="miro_from_tool.gbk" compare="sim_size" delta_frac="0.05">
51 <assert_contents>
52 <has_text text="RBS"/>
53 <has_text text="gene"/>
54 <has_text text="CDS"/>
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[
60 .. class:: warningmark
61
62 This is a LOSSY conversion. This tool **TRUNCATES** genbank file identifiers if
63 they are too long. Your data may not "match up" after processing through this
64 tool.
65
66 **What it does**:
67
68 Convert gff3 data to genbank. There are many WebApollo specific conventions. A re-numbering is also done.
69
70 **Supported / Expected Data**
71
72 - gene / mRNA / (CDS, Exon)
73 - gene / tRNA
74 - terminator
75
76 ]]></help>
77 <expand macro="citations"/>
78 </tool>