diff emboss_5/emboss_pepwheel.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_pepwheel.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
+  <!-- produces png file -->
+  <description>Shows protein sequences as helices</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
+  $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="steps" size="10" type="text" value="18">
+      <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
+    </param>
+    <param name="turns" size="10" type="text" value="5">
+      <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
+    </param>
+    <param name="squares" size="10" type="text" value="ILVM">
+      <label>Residues to mark with squares</label>
+    </param>
+    <param name="diamonds" size="10" type="text" value="DENQST">
+      <label>Residues to mark with diamonds</label>
+    </param>
+    <param name="octags" size="10" type="text" value="HKR">
+      <label>Residues to mark with octagons</label>
+    </param>
+    <param name="wheel" type="select">
+      <label>Plot the wheel</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="amphipathic" type="select">
+      <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>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
+If 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;`_
+  </help>
+</tool>
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