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comparison emboss_seqmatchall.xml @ 10:d49956b87f7e draft

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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
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0.1">
2 <description>All-against-all comparison of a set of sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -aformat2 $out_format1 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="fasta" label="Sequences" />
11 <param name="wordsize" type="integer" value="4" label="Word size" />
12 <param name="out_format1" type="select" label="Output alignment file format">
13 <option value="match">Match (m)</option>
14 <option value="simple">Simple (m)</option>
15 <option value="fasta">FASTA (m)</option>
16 <option value="msf">MSF (m)</option>
17 <option value="srs">SRS (m)</option>
18 <option value="pair">Pair (p)</option>
19 <option value="markx0">Markx0 (p)</option>
20 <option value="markx1">Markx1 (p)</option>
21 <option value="markx2">Markx2 (p)</option>
22 <option value="markx3">Markx3 (p)</option>
23 <option value="markx10">Markx10 (p)</option>
24 <option value="srspair">SRS pair (p)</option>
25 <option value="score">Score (p)</option>
26 <option value="seqmatchall">Seqmatchall Output File</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="out_file1" format="seqmatchall" />
31 </outputs>
32 <tests>
33 <test>
34 <param name="input1" value="2.fasta"/>
35 <param name="wordsize" value="2"/>
36 <param name="out_format1" value="fasta"/>
37 <output name="out_file1" file="emboss_seqmatchall_out.fasta"/>
38 </test>
39 </tests>
40 <help>
41 .. class:: warningmark
42
43 The input dataset needs to be sequences.
44
45 -----
46
47 You can view the original documentation here_.
48
49 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqmatchall.html
50 </help>
51 <expand macro="citations" />
52 </tool>