diff emboss_dotpath.xml @ 11:0e2484b6829b draft

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

--- a/emboss_dotpath.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_dotpath.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,44 +1,31 @@
-<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
-  <description>Non-overlapping wordmatch dotplot of two sequences</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
-  -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>Sequence 1</label>
-    </param>
-    <param format="data" name="input2" type="data">
-      <label>Sequence 2</label>
-    </param>
-    <param name="wordsize" type="text" value="4">
-      <label>Word size (Integer 2 or more)</label>
-    </param>
-    <param name="overlaps" type="select">
-      <label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="boxit" type="select">
-      <label>Draw a box around dotplot</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="png" name="out_file1" />
+<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0.1">
+  <description>Non-overlapping wordmatch dotplot of two sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence 1" />
+    <param name="input2" type="data" format="data" label="Sequence 2" />
+    <param name="wordsize" type="integer" min="2" value="4" label="Word size" />
+    <param name="overlaps" type="select" label="Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="boxit" type="select" label="Draw a box around dotplot">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="png" />
   </outputs>
-  <!-- functional tests not possible since image output contains file name information and timestamp -->
+  <!-- functional tests not possible since image output contains file name information and timestamp -->
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.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/dotpath.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>