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/tools/emboss_5/emboss_fuzzpro.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 50 lines | 46 code | 4 blank | 0 comment | 0 complexity | f07d218358e2923ea789683631592ec0 MD5 | raw file
 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" size="30" type="text" value="">
10      <label>Search pattern</label>
11    </param>
12    <param name="mismatch" size="5" type="text" value="0">
13      <label>Number of mismatches</label>
14    </param>
15    <param name="out_format1" type="select">
16      <label>Output Report File Format</label>
17      <option value="seqtable">SeqTable</option>
18      <option value="embl">EMBL</option>
19      <option value="genbank">GENBANK</option>
20      <option value="gff">GFF</option>
21      <option value="pir">PIR</option>
22      <option value="swiss">SwissProt</option>
23      <option value="dbmotif">DbMotif</option>
24      <option value="diffseq">Diffseq</option>
25      <option value="excel">Excel (tab delimited)</option>
26      <option value="feattable">FeatTable</option>
27      <option value="motif">Motif</option>
28      <option value="regions">Regions</option>
29      <option value="simple">SRS Simple</option>
30      <option value="srs">SRS</option>
31      <option value="table">Table</option>
32      <option value="tagseq">TagSeq</option>
33    </param>
34  </inputs>
35  <outputs>
36    <data format="fuzzpro" name="out_file1" />
37  </outputs>
38  <code file="emboss_format_corrector.py" />
39  <help>
40    You can view the original documentation here_.
41    
42    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html
43
44------
45
46**Citation**
47
48If 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;`_
49  </help>
50</tool>