--- a/DigestorMotif.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/DigestorMotif.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,43 +1,98 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="DigestorMotif" name="DigestorMotif" version="1.12.0">
-  <description>digests a protein database in-silico</description>
-  <macros>
-    <token name="@EXECUTABLE@">DigestorMotif</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>DigestorMotif
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Utilities]-->
+  <tool id="DigestorMotif" name="DigestorMotif" version="2.0.0">
+    <description>digests a protein database in-silico</description>
+    <macros>
+      <token name="@EXECUTABLE@">DigestorMotif</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>DigestorMotif
 
--in ${param_in}
--out ${param_out}
--missed_cleavages ${param_missed_cleavages}
--mass_accuracy ${param_mass_accuracy}
--min_length ${param_min_length}
--out_option ${param_out_option}
--enzyme ${param_enzyme}
--motif ${param_motif}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_missed_cleavages:
+  -missed_cleavages $param_missed_cleavages
+#end if
+#if $param_mass_accuracy:
+  -mass_accuracy $param_mass_accuracy
+#end if
+#if $param_min_length:
+  -min_length $param_min_length
+#end if
+#if $param_out_option:
+  -out_option $param_out_option
+#end if
+#if $param_enzyme:
+  -enzyme
+  #if &quot; &quot; in str($param_enzyme):
+    &quot;$param_enzyme&quot;
+  #else
+    $param_enzyme
+  #end if
+#end if
+#if $param_motif:
+  -motif     &quot;$param_motif&quot;
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in)"/>
-    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages)"/>
-    <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in ppb" help="(-mass_accuracy)"/>
-    <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length)"/>
-    <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option)"/>
-    <param name="param_enzyme" type="text" size="20" value="Trypsin" label="the digestion enzyme" help="(-enzyme)"/>
-    <param name="param_motif" type="text" size="20" value="M" label="the motif for the restricted peptidome" help="(-motif)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file (peptides)#br#" format="idXML"/>
-  </outputs>
-  <help>**What it does**
-
-digests a protein database in-silico
+    <inputs>
+      <param format="fasta" help="(-in) " label="FASTA input file" name="param_in" optional="False" type="data"/>
+      <param help="(-missed_cleavages) " label="the number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/>
+      <param help="(-mass_accuracy) " label="give your mass accuracy in pp" name="param_mass_accuracy" type="integer" value="1000"/>
+      <param help="(-min_length) " label="minimum length of peptide" name="param_min_length" type="integer" value="6"/>
+      <param help="(-out_option) " label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" name="param_out_option" type="integer" value="1"/>
+      <param help="(-enzyme) " label="The enzyme used for peptide digestion" name="param_enzyme" optional="True" type="select" value="Trypsin">
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Trypsin">Trypsin</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="TrypChymo">TrypChymo</option>
+        <option value="V8-E">V8-E</option>
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Lys-C/P">Lys-C/P</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="2-iodobenzoate">2-iodobenzoate</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Lys-C">Lys-C</option>
+        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="PepsinA">PepsinA</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
+        <option value="V8-DE">V8-DE</option>
+        <option value="Arg-C">Arg-C</option>
+      </param>
+      <param help="(-motif) " label="the motif for the restricted peptidome" name="param_motif" size="30" type="text" value="M">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>digests a protein database in-silico
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
+  </tool>