/tools/emboss_5/emboss_matcher.xml

 1<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
 2  <description>Finds the best local alignments between two sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequence 1</label>
 8    </param>
 9    <param format="data" name="input2" type="data">
10      <label>Sequence 2</label>
11    </param>
12    <param name="alternatives" size="4" type="text" value="1">
13      <label>Number of alternative matches</label>
14    </param>
15    <param name="gapopen" size="4" type="text" value="16">
16      <label>Gap penalty</label>
17    </param>
18    <param name="gapextend" size="4" type="text" value="4">
19      <label>Gap length (extension) penalty</label>
20    </param>
21    <param name="out_format1" type="select">
22      <label>Output Alignment File Format</label>
23      <option value="markx0">Markx0 (p)</option>
24      <option value="simple">Simple (m)</option>
25      <option value="fasta">FASTA (m)</option>
26      <option value="msf">MSF (m)</option>
27      <option value="srs">SRS (m)</option>
28      <option value="pair">Pair (p)</option>
29      <option value="markx1">Markx1 (p)</option>
30      <option value="markx2">Markx2 (p)</option>
31      <option value="markx3">Markx3 (p)</option>
32      <option value="markx10">Markx10 (p)</option>
33      <option value="srspair">SRS pair (p)</option>
34      <option value="score">Score (p)</option>
35    </param>
36  </inputs>
37  <outputs>
38    <data format="markx0" name="out_file1" />
39  </outputs>
40  <tests>
41    <test>
42      <param name="input1" value="2.fasta"/>
43      <param name="input2" value="1.fasta"/>
44      <param name="alternatives" value="1"/>
45      <param name="gapopen" value="16"/>
46      <param name="gapextend" value="4"/>
47      <param name="out_format1" value="fasta"/>
48      <output name="out_file1" file="emboss_matcher_out.fasta"/>
49    </test>
50  </tests>
51  <code file="emboss_format_corrector.py" />
52  <help>
53    You can view the original documentation here_.
54    
55    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html
56
57------
58
59**Citation**
60
61If 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;`_
62  </help>
63</tool>