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comparison tools/emboss_5/emboss_fuzznuc.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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" size="5" 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" size="5" 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 </help>
75 </tool>