Mercurial > repos > devteam > emboss_5

comparison emboss_matcher.xml @ 10:d49956b87f7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
parents
children 8992d258e42f
comparison
equal deleted inserted replaced
9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0.1">
2 <description>Finds the best local alignments between two sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>matcher -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="data" label="Sequence 1" />
11 <param name="input2" type="data" format="data" label="Sequence 2" />
12 <param name="alternatives" type="integer" value="1" label="Number of alternative matches" />
13 <param name="gapopen" type="integer" value="16" label="Gap penalty" />
14 <param name="gapextend" type="integer" value="4" label="Gap length (extension) penalty" />
15 <param name="out_format1" type="select" label="Output alignment file format">
16 <option value="markx0">Markx0 (p)</option>
17 <option value="simple">Simple (m)</option>
18 <option value="fasta">FASTA (m)</option>
19 <option value="msf">MSF (m)</option>
20 <option value="srs">SRS (m)</option>
21 <option value="pair">Pair (p)</option>
22 <option value="markx1">Markx1 (p)</option>
23 <option value="markx2">Markx2 (p)</option>
24 <option value="markx3">Markx3 (p)</option>
25 <option value="markx10">Markx10 (p)</option>
26 <option value="srspair">SRS pair (p)</option>
27 <option value="score">Score (p)</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data name="out_file1" format="markx0" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="input1" value="2.fasta"/>
36 <param name="input2" value="1.fasta"/>
37 <param name="alternatives" value="1"/>
38 <param name="gapopen" value="16"/>
39 <param name="gapextend" value="4"/>
40 <param name="out_format1" value="fasta"/>
41 <output name="out_file1" file="emboss_matcher_out.fasta"/>
42 </test>
43 </tests>
44 <help>
45 You can view the original documentation here_.
46
47 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/matcher.html
48 </help>
49 <expand macro="citations" />
50 </tool>