/tools/emboss_5/emboss_newcpgseek.xml

 1<tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0">
 2  <description>Reports CpG rich region</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequence</label>
 8    </param>
 9    <param name="score" size="4" type="text" value="17">
10      <label>CpG score</label>
11    </param>
12  </inputs>
13  <outputs>
14    <data format="newcpgseek" name="out_file1" />
15  </outputs>
16  <tests>
17    <test>
18      <param name="input1" value="2.fasta"/>
19      <param name="score" value="17"/>
20      <output name="out_file1" file="emboss_newcpgseek_out.newcpgseek"/>
21    </test>
22  </tests>
23  <help>
24
25.. class:: warningmark
26
27The input dataset needs to be sequences.
28
29-----
30
31    You can view the original documentation here_.
32    
33    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html
34
35------
36
37**Citation**
38
39If 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;`_
40  </help>
41</tool>