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/tools/emboss_5/emboss_octanol.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 44 lines | 39 code | 4 blank | 1 comment | 0 complexity | cc2eb5739317f10361990a9e02bbf126 MD5 | raw file
 1<tool id="EMBOSS: octanol63" name="octanol" version="5.0.0">
 2  <!-- graphics output with filename, no functional tests added -->  
 3  <description>Displays protein hydropathy</description>
 4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 5  <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
 6  -differenceplot $differenceplot -auto</command>
 7  <inputs>
 8    <param format="data" name="input1" type="data">
 9      <label>Sequences</label>
10    </param>
11    <param name="width" size="4" type="text" value="19">
12      <label>Window size</label>
13    </param>
14    <param name="octanolplot" type="select">
15      <label>Display the octanol plot</label>
16      <option value="no">No</option>
17      <option value="yes">Yes</option>
18    </param>
19    <param name="interfaceplot" type="select">
20      <label>Display the interface plot</label>
21      <option value="no">No</option>
22      <option value="yes">Yes</option>
23    </param>
24    <param name="differenceplot" type="select">
25      <label>Display the difference plot</label>
26      <option value="yes">Yes</option>
27      <option value="no">No</option>
28    </param>
29  </inputs>
30  <outputs>
31    <data format="png" name="out_file1" />
32  </outputs>
33  <help>
34    You can view the original documentation here_.
35    
36    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html
37
38------
39
40**Citation**
41
42If 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;`_
43  </help>
44</tool>