diff emboss_pepinfo.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

--- a/emboss_pepinfo.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_pepinfo.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,36 +1,27 @@
-<tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0">
+<tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0.1">
   <!-- puts file info in output files -->
-  <description>Plots simple amino acid properties in parallel</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>Sequence</label>
-    </param>
-    <param name="hwindow" type="text" value="9">
-      <label>Window size for hydropathy averaging</label>
-    </param>
-    <param name="plot_type" type="select">
-      <label>Choose a plot type</label>
-      <option value="-generalplot yes -hydropathyplot no">Histogram of general properties</option>
-      <option value="-generalplot no -hydropathyplot yes">Graphs of hydropathy</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="pepinfo" name="out_file1" />
-    <data format="png" name="out_file2" />
-  </outputs>
+  <description>Plots simple amino acid properties in parallel</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepinfo -sequence '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -hwindow $hwindow $plot_type -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence" />
+    <param name="hwindow" type="integer" value="9" label="Window size for hydropathy averaging" />
+    <param name="plot_type" type="select" label="Choose a plot type">
+      <option value="-generalplot yes -hydropathyplot no">Histogram of general properties</option>
+      <option value="-generalplot no -hydropathyplot yes">Graphs of hydropathy</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="pepinfo" />
+    <data name="out_file2" format="png" />
+  </outputs>
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.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;`_
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepinfo.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>