diff emboss_polydot.xml @ 11:0e2484b6829b draft

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

--- a/emboss_polydot.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_polydot.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,28 +1,24 @@
-<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0">
+<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1">
   <!-- produces png file, not added functional tests -->
-  <description>Displays all-against-all dotplots of a set of sequences</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
-  $gap -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequence</label>
-    </param>
-    <param name="wordsize" type="text" value="6">
-      <label>Word size</label>
-    </param>
-    <param name="boxit" type="select">
-      <label>Draw a box around each dotplot</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <param name="gap" type="text" value="10">
-      <label>Size of gap</label>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="polydot" name="output1" />
-    <data format="png" name="output2" />
+  <description>Displays all-against-all dotplots of a set of sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
+  $gap -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence" />
+    <param name="wordsize" type="integer" value="6" label="Word size" />
+    <param name="boxit" type="select" label="Draw a box around each dotplot">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="gap" type="integer" value="10" label="Size of gap" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="polydot" />
+    <data name="output2" format="png" />
   </outputs>
 <!--    <tests>
     <test>
@@ -32,9 +28,8 @@
       <param name="gap" value="10"/>
       <output name="output1" file="emboss_polydot_out.png"/>
     </test>
-  </tests>-->
+  </tests>-->
   <help>
-
 .. class:: warningmark
 
 The input dataset needs to be sequences.
@@ -42,15 +37,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.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/polydot.html
   </help>
+  <expand macro="citations" />
 </tool>