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/tools/emboss_5/emboss_pepwheel.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 51 lines | 46 code | 4 blank | 1 comment | 0 complexity | 6e49eb482c8222199f48e86de5d6e7a4 MD5 | raw file
 1<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
 2  <!-- produces png file -->
 3  <description>Shows protein sequences as helices</description>
 4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 5  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
 6  $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
 7  <inputs>
 8    <param format="data" name="input1" type="data">
 9      <label>Sequence</label>
10    </param>
11    <param name="steps" size="10" type="text" value="18">
12      <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
13    </param>
14    <param name="turns" size="10" type="text" value="5">
15      <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
16    </param>
17    <param name="squares" size="10" type="text" value="ILVM">
18      <label>Residues to mark with squares</label>
19    </param>
20    <param name="diamonds" size="10" type="text" value="DENQST">
21      <label>Residues to mark with diamonds</label>
22    </param>
23    <param name="octags" size="10" type="text" value="HKR">
24      <label>Residues to mark with octagons</label>
25    </param>
26    <param name="wheel" type="select">
27      <label>Plot the wheel</label>
28      <option value="yes">Yes</option>
29      <option value="no">No</option>
30    </param>
31    <param name="amphipathic" type="select">
32      <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label>
33      <option value="no">No</option>
34      <option value="yes">Yes</option>
35    </param>
36  </inputs>
37  <outputs>
38    <data format="png" name="out_file1" />
39  </outputs>
40  <help>
41    You can view the original documentation here_.
42    
43    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html
44
45------
46
47**Citation**
48
49If 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;`_
50  </help>
51</tool>