/tools/emboss_5/emboss_plotorf.xml

 1<tool id="EMBOSS: plotorf76" name="plotorf" version="5.0.0">
 2  <!-- produces png file output -->
 3  <description>Plot potential open reading frames</description>
 4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 5  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>
 6  <inputs>
 7    <param format="fasta" name="input1" type="data">
 8      <label>Sequence</label>
 9    </param>
10    <param name="start" size="15" type="text" value="ATG">
11      <label>Start codons</label>
12    </param>
13    <param name="stop" size="15" type="text" value="TAA">
14      <label>Stop codons</label>
15    </param>
16  </inputs>
17  <outputs>
18    <data format="png" name="out_file1" />
19  </outputs>
20  <!--  <tests>
21    <test>
22      <param name="input1" value="2.fasta"/>
23      <param name="start" value="ATG"/>
24      <param name="stop" value="TAA"/>
25      <output name="out_file1" file="emboss_plotorf_out.png"/>
26    </test>
27  </tests> -->
28  <help>
29
30.. class:: warningmark
31
32The input dataset needs to be sequences.
33
34-----
35
36    You can view the original documentation here_.
37    
38    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotorf.html
39
40------
41
42**Citation**
43
44If 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;`_
45  </help>
46</tool>