Mercurial > repos > cpt > cpt_gff_to_gbk

annotate gff2gb.xml @ 4:35a6c466e270 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
author cpt
date Sun, 23 Jul 2023 01:38:52 +0000
parents c8fcb7246ac3
children 03384dbb511d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 <tool id="edu.tamu.cpt.gff.gff2gb" name="GFF3 to GenBank" version="4.0">
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2 <description>convert gff3 to GenBank</description>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 <macros>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
4 <import>macros.xml</import>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
5 <import>cpt-macros.xml</import>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
6 </macros>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 <expand macro="requirements"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9 @GENOME_SELECTOR_PRE@
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 'python $__tool_directory__/gff2gb.py'
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12 @INPUT_GFF@
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 @INPUT_FASTA@
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14 --transltbl '$transltbl'
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15 > '$output']]></command>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16 <inputs>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 <expand macro="input/gff3+fasta"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 <param label="Translation Table" name="transltbl" type="select">
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19 <option value="1">1. The Standard Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20 <option value="2">2. The Vertebrate Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21 <option value="3">3. The Yeast Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 <option value="5">5. The Invertebrate Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
24 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 <option value="10">10. The Euplotid Nuclear Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 <option value="11" selected="true">11. The Bacterial, Archaeal and Plant Plastid Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 <option value="12">12. The Alternative Yeast Nuclear Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29 <option value="13">13. The Ascidian Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31 <option value="16">16. Chlorophycean Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 <option value="21">21. Trematode Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 <option value="24">24. Pterobranchia Mitochondrial Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 </param>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 </inputs>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 <outputs>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40 <data format="genbank" hidden="false" name="output" label="${gff3_data.name} as GenBank"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41 </outputs>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42 <tests>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 <!-- There have been issues running the diffs for the files -->
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 <!-- Going to use asserts and run ONE (or no) diffs -->
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 <test>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 <!-- ORIGINAL TEST FILE, regenerated 10.12.2020 -->
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47 <param name="reference_genome_source" value="history"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48 <param name="genome_fasta" value="miro.fa"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
49 <param name="gff3_data" value="miro.gff3"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
50 <output name="output" file="miro_from_tool.gbk" compare="sim_size" delta_frac="0.05">
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
51 <assert_contents>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
52 <has_text text="RBS"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
53 <has_text text="gene"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
54 <has_text text="CDS"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
55 </assert_contents>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
56 </output>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
57 </test>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
58 </tests>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
59 <help><![CDATA[
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
60 .. class:: warningmark
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
61
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
62 This is a LOSSY conversion. This tool **TRUNCATES** genbank file identifiers if
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
63 they are too long. Your data may not "match up" after processing through this
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
64 tool.
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
65
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
66 **What it does**:
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
67
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
68 Convert gff3 data to genbank. There are many WebApollo specific conventions. A re-numbering is also done.
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
69
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
70 **Supported / Expected Data**
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
71
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
72 - gene / mRNA / (CDS, Exon)
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
73 - gene / tRNA
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
74 - terminator
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
75
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
76 ]]></help>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
77 <expand macro="citations"/>
c8fcb7246ac3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
78 </tool>