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/tools/emboss_5/emboss_newcpgreport.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
 2  <description>Report CpG rich areas</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequence</label>
 8    </param>
 9    <param name="window" size="4" type="text" value="100">
10      <label>Window Size</label>
11    </param>
12    <param name="shift" size="4" type="text" value="1">
13      <label>Step size (shift)</label>
14    </param>
15    <param name="minlen" size="4" type="text" value="200">
16      <label>Minimum length</label>
17    </param>
18    <param name="minoe" size="4" type="text" value="0.6">
19      <label>Minimum average observed to expected ratio</label>
20    </param>
21    <param name="minpc" size="4" type="text" value="50.0">
22      <label>Minimum average percentage of G plus C</label>
23    </param>
24  </inputs>
25  <outputs>
26    <data format="newcpgreport" name="out_file1" />
27  </outputs>
28  <tests>
29    <test>
30      <param name="input1" value="2.fasta"/>
31      <param name="window" value="100"/>
32      <param name="shift" value="1"/>
33      <param name="minlen" value="200"/>
34      <param name="minoe" value="0.6"/>
35      <param name="minpc" value="50.0"/>
36      <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/>
37    </test>
38  </tests>
39  <help>
40    You can view the original documentation here_.
41    
42    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html
43
44------
45
46**Citation**
47
48If 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;`_
49  </help>
50</tool>