/tools/emboss_5/emboss_plotcon.xml

 1<tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0">
 2  <!-- produces png file -->
 3  <description>Plot quality of conservation of a sequence alignment</description>
 4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 5  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>Sequence</label>
 9    </param>
10    <param name="winsize" size="10" type="text" value="4">
11      <label>Number of columns to average alignment quality over</label>
12    </param>
13  </inputs>
14  <outputs>
15    <data format="png" name="out_file1" />
16  </outputs>
17  <help>
18    You can view the original documentation here_.
19    
20    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html
21
22------
23
24**Citation**
25
26If 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;`_
27  </help>
28</tool>