Mercurial > repos > cpt > cpt_gff_to_gbk
comparison cpt_gff_to_gbk/gff2gb.xml @ 0:29014c9867ad draft
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author | cpt |
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date | Fri, 17 Jun 2022 12:54:45 +0000 |
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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> <!-- ORIGINAL TEST FILE, regenerated 10.12.2020 --> | |
46 <param name="reference_genome_source" value="history" /> | |
47 <param name="genome_fasta" value="miro.fa" /> | |
48 <param name="gff3_data" value="miro.gff3" /> | |
49 <output name="output" file="miro_from_tool.gbk" compare="sim_size" delta_frac="0.05"> | |
50 <assert_contents> | |
51 <has_text text="RBS" /> | |
52 <has_text text="gene" /> | |
53 <has_text text="CDS" /> | |
54 </assert_contents> | |
55 </output> | |
56 </test> | |
57 </tests> | |
58 <help><![CDATA[ | |
59 .. class:: warningmark | |
60 | |
61 This is a LOSSY conversion. This tool **TRUNCATES** genbank file identifiers if | |
62 they are too long. Your data may not "match up" after processing through this | |
63 tool. | |
64 | |
65 **What it does**: | |
66 | |
67 Convert gff3 data to genbank. There are many WebApollo specific conventions. A re-numbering is also done. | |
68 | |
69 **Supported / Expected Data** | |
70 | |
71 - gene / mRNA / (CDS, Exon) | |
72 - gene / tRNA | |
73 - terminator | |
74 | |
75 ]]></help> | |
76 <expand macro="citations" /> | |
77 </tool> |