diff emboss_palindrome.xml @ 11:0e2484b6829b draft

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

--- a/emboss_palindrome.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_palindrome.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,31 +1,23 @@
-<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
-  <description>Looks for inverted repeats in a nucleotide sequence</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequences</label>
-    </param>
-    <param name="minpallen" type="text" value="10">
-      <label>Minimum length of palindrome</label>
-    </param>
-    <param name="maxpallen" type="text" value="100">
-      <label>Maximum length of palindrome</label>
-    </param>
-    <param name="gaplimit" type="text" value="100">
-      <label>Maximum gap between repeated regions</label>
-    </param>
-    <param name="nummismatches" type="text" value="0">
-      <label>Number of mismatches allowed</label>
-    </param>
-    <param name="overlap" type="select">
-      <label>Report overlapping matches</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="palindrome" name="out_file1" />
+<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0.1">
+  <description>Looks for inverted repeats in a nucleotide sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" />
+    <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" />
+    <param name="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" />
+    <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" />
+    <param name="overlap" type="select" label="Report overlapping matches">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="palindrome" />
   </outputs>
   <tests>
     <test>
@@ -37,9 +29,8 @@
       <param name="overlap" value="yes"/>
       <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
     </test>
-  </tests>
+  </tests>
   <help>
-
 .. class:: warningmark
 
 The input dataset needs to be sequences.
@@ -47,15 +38,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.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/palindrome.html
   </help>
+  <expand macro="citations" />
 </tool>