--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MassCalculator.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,132 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MassCalculator" name="MassCalculator" version="2.0.0">
+  <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
+  <macros>
+    <token name="@EXECUTABLE@">MassCalculator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MassCalculator
+
+#if $param_in:
+  -in $param_in
+#end if
+
+#if $rep_param_in_seq:
+-in_seq
+  #for token in $rep_param_in_seq:
+    #if " " in str(token):
+      "$token.param_in_seq"
+    #else
+      $token.param_in_seq
+    #end if
+  #end for
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+
+#if $rep_param_charge:
+-charge
+  #for token in $rep_param_charge:
+    #if " " in str(token):
+      "$token.param_charge"
+    #else
+      $token.param_charge
+    #end if
+  #end for
+#end if
+#if $param_format:
+  -format
+  #if " " in str($param_format):
+    "$param_format"
+  #else
+    $param_format
+  #end if
+#end if
+#if $param_average_mass:
+  -average_mass
+#end if
+#if $param_fragment_type:
+  -fragment_type
+  #if " " in str($param_fragment_type):
+    "$param_fragment_type"
+  #else
+    $param_fragment_type
+  #end if
+#end if
+#if $param_separator:
+  -separator     "$param_separator"
+#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="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in) "/>
+    <repeat name="rep_param_in_seq" min="0" title="param_in_seq">
+      <param name="param_in_seq" type="text" size="30" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
+      <param name="param_charge" type="text" size="30" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_format" type="select" optional="True" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="(-format) ">
+      <option value="list">list</option>
+      <option value="table">table</option>
+      <option value="mass_only">mass_only</option>
+      <option value="mz_only">mz_only</option>
+    </param>
+    <param name="param_average_mass" type="boolean" truevalue="-average_mass" falsevalue="" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass) "/>
+    <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) ">
+      <option value="full">full</option>
+      <option value="internal">internal</option>
+      <option value="N-terminal">N-terminal</option>
+      <option value="C-terminal">C-terminal</option>
+      <option value="a-ion">a-ion</option>
+      <option value="b-ion">b-ion</option>
+      <option value="c-ion">c-ion</option>
+      <option value="x-ion">x-ion</option>
+      <option value="y-ion">y-ion</option>
+      <option value="z-ion">z-ion</option>
+    </param>
+    <param name="param_separator" type="text" size="30" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator) ">
+      <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="txt"/>
+  </outputs>
+  <help>**What it does**
+
+Calculates masses and mass-to-charge ratios of peptide sequences
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html</help>
+  <expand macro="references"/>
+</tool>