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comparison fasta_translate.xml @ 1:4cbf9299712b draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:41:52 +0000
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0:cb42bee49abb 1:4cbf9299712b
1 <tool id="edu.tamu.cpt.fasta.seq_trans" name="Fasta Translate" version="19.1.0.0">
2 <description>Translate fasta file</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 '$__tool_directory__/fasta_translate.py'
10 @SEQUENCE@
11
12 --target '${output.format_select}'
13
14 #if str($output.format_select) == "protein":
15 --table '$output.table'
16 '$output.strip_stops'
17 '$output.met'
18 #end if
19
20 > '$default']]></command>
21 <inputs>
22 <expand macro="input/fasta"/>
23 <conditional name="output">
24 <param label="Target output" type="select" name="format_select">
25 <option value="rna">RNA</option>
26 <option value="protein" selected="true">Protein</option>
27 </param>
28 <when value="rna"/>
29 <when value="protein">
30 <param label="Translation table to use" name="table" type="select">
31 <option value="1">[1] The Standard Code</option>
32 <option value="2">[2] The Vertebrate Mitochondrial Code</option>
33 <option value="3">[3] The Yeast Mitochondrial Code</option>
34 <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
35 <option value="5">[5] The Invertebrate Mitochondrial Code </option>
36 <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
37 <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
38 <option value="10">[10] The Euplotid Nuclear Code</option>
39 <option value="11" selected="true">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
40 <option value="12">[12] The Alternative Yeast Nuclear Code</option>
41 <option value="13">[13] The Ascidian Mitochondrial Code</option>
42 <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
43 <option value="15">[15] Blepharisma Nuclear Code</option>
44 <option value="16">[16] Chlorophycean Mitochondrial Code</option>
45 <option value="21">[21] Trematode Mitochondrial Code</option>
46 <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
47 <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
48 <option value="24">[24] Pterobranchia Mitochondrial Code</option>
49 <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
50 </param>
51 <param label="Remove stop characters" name="strip_stops" type="boolean" checked="true" truevalue="--strip_stops" falsevalue=""/>
52 <param label="Convert first residue to Met" name="met" type="boolean" checked="false" truevalue="--met" falsevalue=""/>
53 </when>
54 </conditional>
55 </inputs>
56 <outputs>
57 <data format="fasta" hidden="false" name="default"/>
58 </outputs>
59 <tests>
60 <test>
61 <param name="sequences" value="T7_TranslateIn.fasta"/>
62 <param name="format_select" value="protein"/>
63 <param name="table" value="11"/>
64 <param name="strip_stops" value="--strip_stops"/>
65 <output name="default" file="T7_TranslateOut.fasta"/>
66 </test>
67 </tests>
68 <help><![CDATA[
69 **What it does**
70
71 Translate DNA sequences from an input FASTA or multi-FASTA file to protein or RNA sequences, as selected.
72 ]]></help>
73 <expand macro="citations"/>
74 </tool>