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/tools/emboss_5/emboss_water.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: water107" name="water" version="5.0.0">
 2  <description>Smith-Waterman local alignment</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequence 1</label>
 8    </param>
 9    <param format="fasta" name="input2" type="data">
10      <label>Sequence 2</label>
11    </param>
12    <param name="gapopen" size="6" type="text" value="10.0">
13      <label>Gap open penalty</label>
14    </param>
15    <param name="gapextend" size="6" type="text" value="0.5">
16      <label>Gap extension penalty</label>
17    </param>
18    <param name="brief" type="select">
19      <label>Brief identity and similarity</label>
20      <option value="yes">Yes</option>
21      <option value="no">No</option>
22    </param>
23    <param name="out_format1" type="select">
24      <label>Output Alignment File Format</label>
25      <option value="srs">SRS (m)</option>
26      <option value="simple">Simple (m)</option>
27      <option value="fasta">FASTA (m)</option>
28      <option value="msf">MSF (m)</option>
29      <option value="pair">Pair (p)</option>
30      <option value="markx0">Markx0 (p)</option>
31      <option value="markx1">Markx1 (p)</option>
32      <option value="markx2">Markx2 (p)</option>
33      <option value="markx3">Markx3 (p)</option>
34      <option value="markx10">Markx10 (p)</option>
35      <option value="srspair">SRS pair (p)</option>
36      <option value="score">Score (p)</option>
37    </param>
38  </inputs>
39  <outputs>
40    <data format="srs" name="out_file1" />
41  </outputs>
42  <tests>
43    <test>
44      <param name="input1" value="2.fasta"/>
45      <param name="input2" value="1.fasta"/>
46      <param name="gapopen" value="10.0"/>
47      <param name="gapextend" value="0.5"/>
48      <param name="brief" value="no"/>
49      <param name="out_format1" value="score"/>
50      <output name="out_file1" file="emboss_water_out.score"/>
51    </test>
52  </tests>
53  <code file="emboss_format_corrector.py" />
54  <help>
55
56.. class:: warningmark 
57
58The input datasets need to be sequences. 
59
60----- 
61
62    You can view the original documentation here_.
63    
64    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html
65
66------
67
68**Citation**
69
70If 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;`_
71  </help>
72</tool>