/tools/emboss_5/emboss_dotmatcher.xml

 1<tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0">
 2  <description>Displays a thresholded dotplot of two sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png
 5  -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>Sequence 1</label>
 9    </param>
10    <param format="data" name="input2" type="data">
11      <label>Sequence 2</label>
12    </param>
13    <param name="windowsize" size="4" type="text" value="10">
14      <label>Window size</label>
15    </param>
16    <param name="threshold" size="4" type="text" value="23">
17      <label>Threshold</label>
18    </param>
19  </inputs>
20  <outputs>
21    <data format="png" name="out_file1" />
22  </outputs>
23  <!-- functional tests not possible since image output contains file name information and timestamp -->
24  <help>
25    You can view the original documentation here_.
26    
27    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotmatcher.html
28
29------
30
31**Citation**
32
33If 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;`_
34  </help>
35</tool>