diff emboss_cpgplot.xml @ 11:0e2484b6829b draft

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

--- a/emboss_cpgplot.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_cpgplot.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,41 +1,27 @@
-<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
-  <description>Plot CpG rich areas</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>On query</label>
-    </param>
-    <param name="window" type="integer" value="100">
-      <label>Window Size</label>
-    </param>
-    <param name="minlen" type="integer" value="200">
-      <label>Minimum length</label>
-    </param>
-    <param name="minoe" type="float" value="0.6">
-      <label>Minimum average observed to expected ratio</label>
-    </param>
-    <param name="minpc" type="float" value="50.0">
-      <label>Minimum average percentage of G plus C</label>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="cpgplot" name="outfile" />
-    <data format="png" name="goutfile" />
-    <data format="gff" name="outfeat" />
-  </outputs>
-  <code file="emboss_format_corrector.py" />
+<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
+  <description>Plot CpG rich areas</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>perl '$__tool_directory__/emboss_cpgplot_wrapper.pl' cpgplot -sequence '$input1' -window $window -minlen $minlen -minpc $minpc -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe $minoe -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="On query" />
+    <param name="window" type="integer" value="100" label="Window size" />
+    <param name="minlen" type="integer" value="200" label="Minimum length" />
+    <param name="minoe" type="float" value="0.6" label="Minimum average observed to expected ratio" />
+    <param name="minpc" type="float" value="50.0" label="Minimum average percentage of G plus C" />
+  </inputs>
+  <outputs>
+    <data name="outfile" format="cpgplot" />
+    <data name="goutfile" format="png" />
+    <data name="outfeat" format="gff" />
+  </outputs>
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.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/cpgplot.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>