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/tools/emboss_5/emboss_cpgplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
 2  <description>Plot CpG rich areas</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>On query</label>
 8    </param>
 9    <param name="window" size="4" type="integer" value="100">
10      <label>Window Size</label>
11    </param>
12    <param name="minlen" size="4" type="integer" value="200">
13      <label>Minimum length</label>
14    </param>
15    <param name="minoe" size="4" type="float" value="0.6">
16      <label>Minimum average observed to expected ratio</label>
17    </param>
18    <param name="minpc" size="4" type="float" value="50.0">
19      <label>Minimum average percentage of G plus C</label>
20    </param>
21  </inputs>
22  <outputs>
23    <data format="cpgplot" name="outfile" />
24    <data format="png" name="goutfile" />
25    <data format="gff" name="outfeat" />
26  </outputs>
27  <code file="emboss_format_corrector.py" />
28  <help>
29    You can view the original documentation here_.
30    
31    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html
32
33------
34
35**Citation**
36
37If 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;`_
38  </help>
39</tool>