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/tools/emboss_5/emboss_dottup.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 36 lines | 31 code | 4 blank | 1 comment | 0 complexity | ff14c95b15d0d84c6160db2cd7440950 MD5 | raw file
 1<tool id="EMBOSS: dottup26" name="dottup" version="5.0.0">
 2  <description>Displays a wordmatch 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 dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png  -xygraph png -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequence 1</label>
 8    </param>
 9    <param format="data" name="input2" type="data">
10      <label>Sequence 2</label>
11    </param>
12    <param name="wordsize" size="4" type="text" value="4">
13      <label>Word size</label>
14    </param>
15    <param name="boxit" type="select">
16      <label>Draw a box around dotplot</label>
17      <option value="yes">Yes</option>
18      <option value="no">No</option>
19    </param>
20  </inputs>
21  <outputs>
22    <data format="png" name="out_file1" />
23  </outputs>
24  <!-- functional tests not possible since image output contains file name information and timestamp -->
25  <help>
26    You can view the original documentation here_.
27    
28    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html
29
30------
31
32**Citation**
33
34If 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;`_
35  </help>
36</tool>