diff emboss_etandem.xml @ 11:0e2484b6829b draft

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

--- a/emboss_etandem.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_etandem.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,53 +1,46 @@
-<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
-  <description>Looks for tandem repeats in a nucleotide sequence</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequence</label>
-    </param>
-    <param name="minrepeat" type="text" value="10">
-      <label>Minimum repeat size</label>
-    </param>
-    <param name="maxrepeat" type="text" value="10">
-      <label>Maximum repeat size</label>
-    </param>
-    <param name="threshold" type="text" value="20">
-      <label>Threshold score</label>
-    </param>
-    <param name="mismatch" type="select">
-      <label>Allow N as a mismatch</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="uniform" type="select">
-      <label>Allow uniform consensus</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="out_format1" type="select">
-      <label>Output Report File Format</label>
-      <option value="table">Table</option>
-      <option value="embl">EMBL</option>
-      <option value="genbank">GENBANK</option>
-      <option value="gff">GFF</option>
-      <option value="pir">PIR</option>
-      <option value="swiss">SwissProt</option>
-      <option value="dbmotif">DbMotif</option>
-      <option value="diffseq">Diffseq</option>
-      <option value="excel">Excel (tab delimited)</option>
-      <option value="feattable">FeatTable</option>
-      <option value="motif">Motif</option>
-      <option value="regions">Regions</option>
-      <option value="seqtable">SeqTable</option>
-      <option value="simple">SRS Simple</option>
-      <option value="srs">SRS</option>
-      <option value="tagseq">TagSeq</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="etandem" name="out_file1" />
-    <data format="table" name="ofile2" />    
+<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0.1">
+  <description>Looks for tandem repeats in a nucleotide sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence" />
+    <param name="minrepeat" type="integer" value="10" label="Minimum repeat size" />
+    <param name="maxrepeat" type="integer" value="10" label="Maximum repeat size" />
+    <param name="threshold" type="integer" value="20" label="Threshold score" />
+    <param name="mismatch" type="select" label="Allow N as a mismatch">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="uniform" type="select" label="Allow uniform consensus">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <option value="table">Table</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="etandem" />
+    <data name="ofile2" format="table" />
   </outputs>
     <tests>
     <test>
@@ -60,8 +53,7 @@
       <param name="out_format1" value="table"/>
       <output name="ofile2" file="emboss_etandem_out.table"/>
     </test>
-  </tests>
-  <code file="emboss_format_corrector.py" />
+  </tests>
   <help>
 .. class:: warningmark
 
@@ -70,17 +62,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.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/etandem.html
   </help>
+  <expand macro="citations" />
 </tool>
-
-