diff emboss_einverted.xml @ 11:0e2484b6829b draft

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

--- a/emboss_einverted.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_einverted.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,29 +1,20 @@
-<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
-  <description>Finds DNA inverted repeats</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>On query</label>
-    </param>
-    <param name="gap" type="text" value="12">
-      <label>Gap penalty</label>
-    </param>
-    <param name="threshold" type="text" value="50">
-      <label>Minimum score threshold</label>
-    </param>
-    <param name="match" type="text" value="3">
-      <label>Match score</label>
-    </param>
-    <param name="mismatch" type="text" value="-4">
-      <label>Mismatch score</label>
-    </param>
-    <param name="maxrepeat" type="text" value="2000">
-      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="einverted" name="out_file1" />
+<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0.1">
+  <description>Finds DNA inverted repeats</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="On query" />
+    <param name="gap" type="integer" value="12" label="Gap penalty" />
+    <param name="threshold" type="integer" value="50" label="Minimum score threshold" />
+    <param name="match" type="integer" value="3" label="Match score" />
+    <param name="mismatch" type="integer" value="-4" label="Mismatch score" />
+    <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" />
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="einverted" />
   </outputs>
   <tests>
     <test>
@@ -35,7 +26,7 @@
       <param name="maxrepeat" value="2000"/>
       <output name="out_file1" file="emboss_einverted_out.einverted"/>
     </test>
-  </tests>
+  </tests>
   <help>
 .. class:: warningmark
 
@@ -44,15 +35,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.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/einverted.html
   </help>
+  <expand macro="citations" />
 </tool>