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/tools/emboss_5/emboss_wordmatch.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 80 lines | 61 code | 8 blank | 11 comment | 0 complexity | 490e45a68d84f57b72b3b3f2cbbbc31a MD5 | raw file
 1<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
 2  <description>Finds all exact matches of a given size between 2 sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
 5  -offormat5 $out_format3 -auto</command>
 6  <inputs>
 7    <param format="fasta" name="input1" type="data">
 8      <label>Sequence 1</label>
 9    </param>
10    <param format="fasta" name="input2" type="data">
11      <label>Sequence 2</label>
12    </param>
13    <param name="wordsize" size="5" type="text" value="4">
14      <label>Word size</label>
15    </param>
16    <param name="out_format1" type="select">
17      <label>Output Alignment File Format</label>
18      <option value="match">Match (m)</option>
19      <option value="simple">Simple (m)</option>
20      <option value="fasta">FASTA (m)</option>
21      <option value="msf">MSF (m)</option>
22      <option value="srs">SRS (m)</option>
23      <option value="pair">Pair (p)</option>
24      <option value="markx0">Markx0 (p)</option>
25      <option value="markx1">Markx1 (p)</option>
26      <option value="markx2">Markx2 (p)</option>
27      <option value="markx3">Markx3 (p)</option>
28      <option value="markx10">Markx10 (p)</option>
29      <option value="srspair">SRS pair (p)</option>
30      <option value="score">Score (p)</option>
31    </param>
32    <param name="out_format2" type="select">
33      <label>Output Feature 1 File Format</label>
34      <option value="gff">GFF</option>
35      <option value="embl">EMBL</option>
36      <option value="swiss">SwissProt</option>
37    </param>
38    <param name="out_format3" type="select">
39      <label>Output Feature 2 File Format</label>
40      <option value="gff">GFF</option>
41      <option value="embl">EMBL</option>
42      <option value="swiss">SwissProt</option>
43    </param>
44  </inputs>
45  <outputs>
46    <data format="match" name="out_file1" />
47    <data format="gff" name="out_file2" />
48    <data format="gff" name="out_file3" />
49  </outputs>
50  <!--   <tests>
51    <test>
52      <param name="input1" value="2.fasta"/>
53      <param name="input2" value="1.fasta"/>
54      <param name="wordsize" value="4"/>
55      <param name="out_format1" value="fasta"/>
56      <param name="out_format2" value="gff"/>
57      <param name="out_format3" value="gff"/>
58      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
59    </test> 
60  </tests> test takes a long time to run-->
61  <code file="emboss_format_corrector.py" />
62  <help>
63
64.. class:: warningmark 
65
66The input datasets need to be sequences. 
67
68----- 
69
70    You can view the original documentation here_.
71    
72    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
73
74------
75
76**Citation**
77
78If 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;`_
79  </help>
80</tool>