diff emboss_supermatcher.xml @ 11:0e2484b6829b draft

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

--- a/emboss_supermatcher.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_supermatcher.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,47 +1,38 @@
-<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
+<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0.1">
   <!-- puts file information in output report -->
-  <description>Match large sequences against one or more other sequences</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
-  $out_format1 -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Large sequences</label>
-    </param>
-    <param format="data" name="input2" type="data">
-      <label>Sequences to match</label>
-    </param>
-    <param name="gapopen" type="text" value="10.0">
-      <label>Gap opening penalty</label>
-    </param>
-    <param name="gapextend" type="text" value="0.5">
-      <label>Gap extension penalty</label>
-    </param>
-    <param name="width" type="text" value="16">
-      <label>Alignment width</label>
-    </param>
-    <param name="wordlen" type="text" value="6">
-      <label>Word length for initial matching</label>
-    </param>
-    <param name="out_format1" type="select">
-      <label>Output Alignment File Format</label>
-      <option value="simple">Simple (m)</option>
-      <option value="fasta">FASTA (m)</option>
-      <option value="msf">MSF (m)</option>
-      <option value="srs">SRS (m)</option>
-      <option value="pair">Pair (p)</option>
-      <option value="markx0">Markx0 (p)</option>
-      <option value="markx1">Markx1 (p)</option>
-      <option value="markx2">Markx2 (p)</option>
-      <option value="markx3">Markx3 (p)</option>
-      <option value="markx10">Markx10 (p)</option>
-      <option value="srspair">SRS pair (p)</option>
-      <option value="score">Score (p)</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="simple" name="ofile1" />
-    <data format="supermatcher" name="ofile2" />
+  <description>Match large sequences against one or more other sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3
+  $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Large sequences" />
+    <param name="input2" type="data" format="data" label="Sequences to match" />
+    <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" />
+    <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
+    <param name="width" type="integer" value="16" label="Alignment width" />
+    <param name="wordlen" type="integer" value="6" label="Word length for initial matching" />
+    <param name="out_format1" type="select" label="Output alignment file format">
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="ofile1" format="simple" />
+    <data name="ofile2" format="supermatcher" />
   </outputs>
 <!--    <tests>
     <test>
@@ -54,19 +45,11 @@
       <param name="out_format1" value="fasta"/>
       <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
     </test>
-  </tests> -->
-  <code file="emboss_format_corrector.py" />
+  </tests> -->
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.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/supermatcher.html
   </help>
+  <expand macro="citations" />
 </tool>