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comparison emboss_fuzznuc.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: fuzznuc37" name="fuzznuc" version="5.0.1">
2 <description>Nucleic acid pattern search</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -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 <sanitizer>
12 <valid initial="string.printable">
13 <remove value="&apos;"/>
14 </valid>
15 <mapping initial="none">
16 <add source="&apos;" target=""/>
17 </mapping>
18 </sanitizer>
19 </param>
20 <param name="mismatch" type="text" value="0">
21 <label>Number of mismatches</label>
22 </param>
23 <param name="complement" type="select">
24 <label>Search complementary strand</label>
25 <option value="no">No</option>
26 <option value="yes">Yes</option>
27 </param>
28 <param name="out_format1" type="select">
29 <label>Output Report File Format</label>
30 <option value="seqtable">SeqTable</option>
31 <option value="embl">EMBL</option>
32 <option value="genbank">GENBANK</option>
33 <option value="gff">GFF</option>
34 <option value="pir">PIR</option>
35 <option value="swiss">SwissProt</option>
36 <option value="dbmotif">DbMotif</option>
37 <option value="diffseq">Diffseq</option>
38 <option value="excel">Excel (tab delimited)</option>
39 <option value="feattable">FeatTable</option>
40 <option value="motif">Motif</option>
41 <option value="regions">Regions</option>
42 <option value="simple">SRS Simple</option>
43 <option value="fuzznuc">Fuzznuc Output File</option>
44 <option value="srs">SRS</option>
45 <option value="table">Table</option>
46 <option value="tagseq">TagSeq</option>
47 </param>
48 </inputs>
49 <outputs>
50 <data format="fuzznuc" name="out_file1" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="input1" value="2.fasta"/>
55 <param name="pattern" value="AA"/>
56 <param name="mismatch" value="0"/>
57 <param name="complement" value="no"/>
58 <param name="out_format1" value="excel"/>
59 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
60 </test>
61 </tests>
62 <code file="emboss_format_corrector.py" />
63 <help>
64
65 .. class:: warningmark
66
67 The input dataset needs to be sequences.
68
69 -----
70
71 You can view the original documentation here_.
72
73 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html
74
75 ------
76
77 **Citation**
78
79 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;`_
80
81 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;`_
82 </help>
83 </tool>