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comparison emboss_fuzztran.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1">
2 <description>Protein pattern search after translation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="fasta" label="Sequences" />
11 <param name="pattern" type="text" value="" label="Search pattern" />
12 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
13 <param name="frame" type="select" label="Frame(s) to translate">
14 <option value="1">Frame 1</option>
15 <option value="2">Frame 2</option>
16 <option value="3">Frame 3</option>
17 <option value="F">Forward three frames</option>
18 <option value="-1">Frame -1</option>
19 <option value="-2">Frame -2</option>
20 <option value="-3">Frame -3</option>
21 <option value="R">Reverse three frames</option>
22 <option value="6">All six frames</option>
23 </param>
24 <param name="table" type="select" label="Code to use">
25 <option value="0">Standard</option>
26 <option value="1">Standard (with alternative initiation codons)</option>
27 <option value="2">Vertebrate Mitochondrial</option>
28 <option value="3">Yeast Mitochondrial</option>
29 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
30 <option value="5">Invertebrate Mitochondrial</option>
31 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
32 <option value="9">Echinoderm Mitochondrial</option>
33 <option value="10">Euplotid Nuclear</option>
34 <option value="11">Bacterial</option>
35 <option value="12">Alternative Yeast Nuclear</option>
36 <option value="13">Ascidian Mitochondrial</option>
37 <option value="14">Flatworm Mitochondrial</option>
38 <option value="15">Blepharisma Macronuclear</option>
39 <option value="16">Chlorophycean Mitochondrial</option>
40 <option value="21">Trematode Mitochondrial</option>
41 <option value="22">Scenedesmus obliquus</option>
42 <option value="23">Thraustochytrium Mitochondrial</option>
43 </param>
44 <param name="out_format1" type="select" label="Output report file format">
45 <option value="table">Table</option>
46 <option value="embl">EMBL</option>
47 <option value="genbank">GENBANK</option>
48 <option value="gff">GFF</option>
49 <option value="pir">PIR</option>
50 <option value="swiss">SwissProt</option>
51 <option value="dbmotif">DbMotif</option>
52 <option value="diffseq">Diffseq</option>
53 <option value="excel">Excel (tab delimited)</option>
54 <option value="feattable">FeatTable</option>
55 <option value="motif">Motif</option>
56 <option value="regions">Regions</option>
57 <option value="seqtable">SeqTable</option>
58 <option value="simple">SRS Simple</option>
59 <option value="srs">SRS</option>
60 <option value="tagseq">TagSeq</option>
61 </param>
62 </inputs>
63 <outputs>
64 <data name="out_file1" format="fuzztran" />
65 </outputs>
66 <tests>
67 <test>
68 <param name="input1" value="1.fasta"/>
69 <param name="pattern" value="AA"/>
70 <param name="mismatch" value="0"/>
71 <param name="frame" value="6"/>
72 <param name="table" value="0"/>
73 <param name="out_format1" value="excel"/>
74 <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
75 </test>
76 </tests>
77 <help>
78 .. class:: warningmark
79
80 The input dataset needs to be sequences.
81
82 -----
83
84 You can view the original documentation here_.
85
86 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzztran.html
87 </help>
88 <expand macro="citations" />
89 </tool>