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comparison emboss_fuzztran.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
2 <description>Protein pattern search after translation</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>Sequences</label>
8 </param>
9 <param name="pattern" type="text" value="">
10 <label>Search pattern</label>
11 </param>
12 <param name="mismatch" type="text" value="0">
13 <label>Number of mismatches</label>
14 </param>
15 <param name="frame" type="select">
16 <label>Frame(s) to translate</label>
17 <option value="1">Frame 1</option>
18 <option value="2">Frame 2</option>
19 <option value="3">Frame 3</option>
20 <option value="F">Forward three frames</option>
21 <option value="-1">Frame -1</option>
22 <option value="-2">Frame -2</option>
23 <option value="-3">Frame -3</option>
24 <option value="R">Reverse three frames</option>
25 <option value="6">All six frames</option>
26 </param>
27 <param name="table" type="select">
28 <label>Code to use</label>
29 <option value="0">Standard</option>
30 <option value="1">Standard (with alternative initiation codons)</option>
31 <option value="2">Vertebrate Mitochondrial</option>
32 <option value="3">Yeast Mitochondrial</option>
33 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
34 <option value="5">Invertebrate Mitochondrial</option>
35 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
36 <option value="9">Echinoderm Mitochondrial</option>
37 <option value="10">Euplotid Nuclear</option>
38 <option value="11">Bacterial</option>
39 <option value="12">Alternative Yeast Nuclear</option>
40 <option value="13">Ascidian Mitochondrial</option>
41 <option value="14">Flatworm Mitochondrial</option>
42 <option value="15">Blepharisma Macronuclear</option>
43 <option value="16">Chlorophycean Mitochondrial</option>
44 <option value="21">Trematode Mitochondrial</option>
45 <option value="22">Scenedesmus obliquus</option>
46 <option value="23">Thraustochytrium Mitochondrial</option>
47 </param>
48 <param name="out_format1" type="select">
49 <label>Output Report File Format</label>
50 <option value="table">Table</option>
51 <option value="embl">EMBL</option>
52 <option value="genbank">GENBANK</option>
53 <option value="gff">GFF</option>
54 <option value="pir">PIR</option>
55 <option value="swiss">SwissProt</option>
56 <option value="dbmotif">DbMotif</option>
57 <option value="diffseq">Diffseq</option>
58 <option value="excel">Excel (tab delimited)</option>
59 <option value="feattable">FeatTable</option>
60 <option value="motif">Motif</option>
61 <option value="regions">Regions</option>
62 <option value="seqtable">SeqTable</option>
63 <option value="simple">SRS Simple</option>
64 <option value="srs">SRS</option>
65 <option value="tagseq">TagSeq</option>
66 </param>
67 </inputs>
68 <outputs>
69 <data format="fuzztran" name="out_file1" />
70 </outputs>
71 <tests>
72 <test>
73 <param name="input1" value="1.fasta"/>
74 <param name="pattern" value="AA"/>
75 <param name="mismatch" value="0"/>
76 <param name="frame" value="6"/>
77 <param name="table" value="0"/>
78 <param name="out_format1" value="excel"/>
79 <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
80 </test>
81 </tests>
82 <code file="emboss_format_corrector.py" />
83 <help>
84
85 .. class:: warningmark
86
87 The input dataset needs to be sequences.
88
89 -----
90
91 You can view the original documentation here_.
92
93 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
94
95 ------
96
97 **Citation**
98
99 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
100
101 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
102 </help>
103 </tool>