--- a/emboss_fuzztran.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_fuzztran.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,72 +1,67 @@
-<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
-  <description>Protein pattern search after translation</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequences</label>
-    </param>
-    <param name="pattern" type="text" value="">
-      <label>Search pattern</label>
-    </param>
-    <param name="mismatch" type="text" value="0">
-      <label>Number of mismatches</label>
-    </param>
-    <param name="frame" type="select">
-      <label>Frame(s) to translate</label>
-      <option value="1">Frame 1</option>
-      <option value="2">Frame 2</option>
-      <option value="3">Frame 3</option>
-      <option value="F">Forward three frames</option>
-      <option value="-1">Frame -1</option>
-      <option value="-2">Frame -2</option>
-      <option value="-3">Frame -3</option>
-      <option value="R">Reverse three frames</option>
-      <option value="6">All six frames</option>
-    </param>
-    <param name="table" type="select">
-      <label>Code to use</label>
-      <option value="0">Standard</option>
-      <option value="1">Standard (with alternative initiation codons)</option>
-      <option value="2">Vertebrate Mitochondrial</option>
-      <option value="3">Yeast Mitochondrial</option>
-      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
-      <option value="5">Invertebrate Mitochondrial</option>
-      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
-      <option value="9">Echinoderm Mitochondrial</option>
-      <option value="10">Euplotid Nuclear</option>
-      <option value="11">Bacterial</option>
-      <option value="12">Alternative Yeast Nuclear</option>
-      <option value="13">Ascidian Mitochondrial</option>
-      <option value="14">Flatworm Mitochondrial</option>
-      <option value="15">Blepharisma Macronuclear</option>
-      <option value="16">Chlorophycean Mitochondrial</option>
-      <option value="21">Trematode Mitochondrial</option>
-      <option value="22">Scenedesmus obliquus</option>
-      <option value="23">Thraustochytrium Mitochondrial</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="fuzztran" name="out_file1" />
+<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1">
+  <description>Protein pattern search after translation</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="pattern" type="text" value="" label="Search pattern" />
+    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
+    <param name="frame" type="select" label="Frame(s) to translate">
+      <option value="1">Frame 1</option>
+      <option value="2">Frame 2</option>
+      <option value="3">Frame 3</option>
+      <option value="F">Forward three frames</option>
+      <option value="-1">Frame -1</option>
+      <option value="-2">Frame -2</option>
+      <option value="-3">Frame -3</option>
+      <option value="R">Reverse three frames</option>
+      <option value="6">All six frames</option>
+    </param>
+    <param name="table" type="select" label="Code to use">
+      <option value="0">Standard</option>
+      <option value="1">Standard (with alternative initiation codons)</option>
+      <option value="2">Vertebrate Mitochondrial</option>
+      <option value="3">Yeast Mitochondrial</option>
+      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+      <option value="5">Invertebrate Mitochondrial</option>
+      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
+      <option value="9">Echinoderm Mitochondrial</option>
+      <option value="10">Euplotid Nuclear</option>
+      <option value="11">Bacterial</option>
+      <option value="12">Alternative Yeast Nuclear</option>
+      <option value="13">Ascidian Mitochondrial</option>
+      <option value="14">Flatworm Mitochondrial</option>
+      <option value="15">Blepharisma Macronuclear</option>
+      <option value="16">Chlorophycean Mitochondrial</option>
+      <option value="21">Trematode Mitochondrial</option>
+      <option value="22">Scenedesmus obliquus</option>
+      <option value="23">Thraustochytrium Mitochondrial</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="fuzztran" />
   </outputs>
   <tests>
     <test>
@@ -78,10 +73,8 @@
       <param name="out_format1" value="excel"/>
       <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
     </test>
-  </tests>
-  <code file="emboss_format_corrector.py" />
+  </tests>
   <help>
-
 .. class:: warningmark
 
 The input dataset needs to be sequences.
@@ -89,15 +82,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.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/fuzztran.html
   </help>
+  <expand macro="citations" />
 </tool>