PageRenderTime 24ms CodeModel.GetById 15ms app.highlight 4ms RepoModel.GetById 1ms app.codeStats 0ms

/tools/emboss_5/emboss_fuzznuc.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 81 lines | 73 code | 8 blank | 0 comment | 0 complexity | 4faea9ac37c2d4e9f424d5a5737348f1 MD5 | raw file
 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
67The 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
79If 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;`_
80  </help>
81</tool>