diff emboss_oddcomp.xml @ 11:0e2484b6829b draft

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

--- a/emboss_oddcomp.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_oddcomp.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,27 +1,22 @@
-<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
+<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1">
   <!-- output contains file location info, commented out functional tests -->
-  <description>Find protein sequence regions with a biased composition</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>Sequences</label>
-    </param>
-    <param format="data" name="input2" type="data">
-      <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
-    </param>
-    <param name="window" type="text" value="30">
-      <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
-    </param>
-    <param name="ignorebz" type="select">
-      <label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words
-      containing them, just noting them in the count of 'Other' words</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="oddcomp" name="out_file1" />
+  <description>Find protein sequence regions with a biased composition</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequences" />
+    <param name="input2" type="data" format="data" label="Dataset in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis" />
+    <param name="window" type="integer" value="30" label="Size of window in which to count" help="If you want to count frequencies in a 40 aa stretch you should enter 40 here" />
+    <param name="ignorebz" type="select" label="Ignore B and Z" help="The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="oddcomp" />
   </outputs>
 <!--    <tests>
     <test>
@@ -31,18 +26,11 @@
       <param name="ignorebz" value="yes"/>
       <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
     </test>
-  </tests> -->
+  </tests> -->
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.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/oddcomp.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>