--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DigestorMotif.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,79 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>DigestorMotif
+
+#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 $param_enzyme:
+  -enzyme     "$param_enzyme"
+#end if
+#if $param_motif:
+  -motif     "$param_motif"
+#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 pp" 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="30" value="Trypsin" label="the digestion enzyme" help="(-enzyme) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+  </outputs>
+  <help>**What it does**
+
+digests a protein database in-silico
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
+  <expand macro="references"/>
+</tool>