--- a/AdditiveSeries.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/AdditiveSeries.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,49 +1,109 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="AdditiveSeries" name="AdditiveSeries" version="1.12.0">
-  <description>Computes an additive series to quantify a peptide in a set of samples.</description>
-  <macros>
-    <token name="@EXECUTABLE@">AdditiveSeries</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>AdditiveSeries
+<?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: [Quantitation]-->
+  <tool id="AdditiveSeries" name="AdditiveSeries" version="2.0.0">
+    <description>Computes an additive series to quantify a peptide in a set of samples.</description>
+    <macros>
+      <token name="@EXECUTABLE@">AdditiveSeries</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>AdditiveSeries
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_mz_tolerance:
+  -mz_tolerance $param_mz_tolerance
+#end if
+#if $param_rt_tolerance:
+  -rt_tolerance $param_rt_tolerance
+#end if
 
--in ${param_in}
--out ${param_out}
--mz_tolerance ${param_mz_tolerance}
--rt_tolerance ${param_rt_tolerance}
--concentrations ${param_concentrations}
--feature_rt ${param_feature_rt}
--feature_mz ${param_feature_mz}
--standard_rt ${param_standard_rt}
--standard_mz ${param_standard_mz}
--threads \${GALAXY_SLOTS:-24} 
-${param_write_gnuplot_output}
--plot:out_gp ${param_out_gp}
+#if $rep_param_concentrations:
+-concentrations
+  #for token in $rep_param_concentrations:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_concentrations&quot;
+    #else
+      $token.param_concentrations
+    #end if
+  #end for
+#end if
+#if $param_feature_rt:
+  -feature_rt $param_feature_rt
+#end if
+#if $param_feature_mz:
+  -feature_mz $param_feature_mz
+#end if
+#if $param_standard_rt:
+  -standard_rt $param_standard_rt
+#end if
+#if $param_standard_mz:
+  -standard_mz $param_standard_mz
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_plot_write_gnuplot_output:
+  -plot:write_gnuplot_output
+#end if
+#if $param_plot_out_gp:
+  -plot:out_gp     &quot;$param_plot_out_gp&quot;
+#end if
+#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="featureXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
-    <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance)"/>
-    <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance)"/>
-    <param name="param_concentrations" type="text" size="20" value="0" label="List of spiked concentrations" help="(-concentrations)"/>
-    <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt)"/>
-    <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz)"/>
-    <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt)"/>
-    <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz)"/>
-    <param name="param_write_gnuplot_output" type="boolean" truevalue="-plot:write_gnuplot_output true" falsevalue="-plot:write_gnuplot_output false" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output)"/>
-    <param name="param_out_gp" type="text" size="20" label="base file name (3 files with different extensions are created)" help="(-out_gp)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output XML file containg regression line and confidence interval" format="xml"/>
-  </outputs>
-  <help>**What it does**
-
-Computes an additive series to quantify a peptide in a set of samples.
+    <inputs>
+      <param format="xml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-mz_tolerance) " label="Tolerance in m/z dimension" name="param_mz_tolerance" type="float" value="1.0"/>
+      <param help="(-rt_tolerance) " label="Tolerance in RT dimension" name="param_rt_tolerance" type="float" value="1.0"/>
+      <repeat min="1" name="rep_param_concentrations" title="param_concentrations">
+        <param help="(-concentrations) " label="List of spiked concentrations" name="param_concentrations" size="30" type="text" value="0">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-feature_rt) " label="RT position of the feature" name="param_feature_rt" type="float" value="-1.0"/>
+      <param help="(-feature_mz) " label="m/z position of the feature" name="param_feature_mz" type="float" value="-1.0"/>
+      <param help="(-standard_rt) " label="RT position of the standard" name="param_standard_rt" type="float" value="-1.0"/>
+      <param help="(-standard_mz) " label="m/z position of the standard" name="param_standard_mz" type="float" value="-1.0"/>
+      <param checked="false" falsevalue="" help="(-write_gnuplot_output) " label="Flag that activates the GNUplot output" name="param_plot_write_gnuplot_output" optional="True" truevalue="-plot:write_gnuplot_output" type="boolean"/>
+      <param help="(-out_gp) " label="base file name (3 files with different extensions are created)" name="param_plot_out_gp" size="30" type="text">
+        <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>Computes an additive series to quantify a peptide in a set of samples.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
+  </tool>