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comparison emboss_fuzzpro.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: fuzzpro38" name="fuzzpro" version="5.0.0">
2 <description>Protein pattern search</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
5 <inputs>
6 <param format="data" name="input1" type="data">
7 <label>Sequences</label>
8 </param>
9 <param name="pattern" type="text" value="">
10 <sanitizer>
11 <valid initial="string.printable">
12 <remove value="&apos;"/>
13 </valid>
14 <mapping initial="none">
15 <add source="&apos;" target=""/>
16 </mapping>
17 </sanitizer>
18 <label>Search pattern</label>
19 </param>
20 <param name="mismatch" type="text" value="0">
21 <label>Number of mismatches</label>
22 </param>
23 <param name="out_format1" type="select">
24 <label>Output Report File Format</label>
25 <option value="seqtable">SeqTable</option>
26 <option value="embl">EMBL</option>
27 <option value="genbank">GENBANK</option>
28 <option value="gff">GFF</option>
29 <option value="pir">PIR</option>
30 <option value="swiss">SwissProt</option>
31 <option value="dbmotif">DbMotif</option>
32 <option value="diffseq">Diffseq</option>
33 <option value="excel">Excel (tab delimited)</option>
34 <option value="feattable">FeatTable</option>
35 <option value="motif">Motif</option>
36 <option value="regions">Regions</option>
37 <option value="simple">SRS Simple</option>
38 <option value="srs">SRS</option>
39 <option value="table">Table</option>
40 <option value="tagseq">TagSeq</option>
41 </param>
42 </inputs>
43 <outputs>
44 <data format="fuzzpro" name="out_file1" />
45 </outputs>
46 <code file="emboss_format_corrector.py" />
47 <help>
48 You can view the original documentation here_.
49
50 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html
51
52 ------
53
54 **Citation**
55
56 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;`_
57
58 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;`_
59 </help>
60 </tool>