--- a/RTPredict.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/RTPredict.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,51 +1,73 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="RTPredict" name="RTPredict" version="1.12.0">
-  <description>Predicts retention times for peptides using a model trained by RTModel.</description>
-  <macros>
-    <token name="@EXECUTABLE@">RTPredict</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>RTPredict
+<?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: [Peptide property prediction]-->
+  <tool id="RTPredict" name="RTPredict" version="2.0.0">
+    <description>Predicts retention times for peptides using a model trained by RTModel.</description>
+    <macros>
+      <token name="@EXECUTABLE@">RTPredict</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>RTPredict
 
--in_id ${param_in_id}
--in_text ${param_in_text}
--svm_model ${param_svm_model}
--total_gradient_time ${param_total_gradient_time}
--threads \${GALAXY_SLOTS:-24} 
--out_id:file ${param_file}
--out_id:positive ${param_positive}
--out_id:negative ${param_negative}
--out_text:file ${param_file}
+#if $param_in_id:
+  -in_id $param_in_id
+#end if
+#if $param_in_text:
+  -in_text $param_in_text
+#end if
+#if $param_svm_model:
+  -svm_model $param_svm_model
+#end if
+#if $param_total_gradient_time:
+  -total_gradient_time $param_total_gradient_time
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_out_id_file:
+  -out_id:file $param_out_id_file
+#end if
+#if $param_out_id_positive:
+  -out_id:positive $param_out_id_positive
+#end if
+#if $param_out_id_negative:
+  -out_id:negative $param_out_id_negative
+#end if
+#if $param_out_text_file:
+  -out_text:file $param_out_text_file
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -max_number_of_peptides ${adv_opts.param_max_number_of_peptides}
-    ${adv_opts.param_rewrite_peptideidentification_rtmz}
+    #if $adv_opts.param_max_number_of_peptides:
+  -max_number_of_peptides $adv_opts.param_max_number_of_peptides
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
+  -out_id:rewrite_peptideidentification_rtmz
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in_id" type="data" format="idXML" optional="True" label="Peptides with precursor information" help="(-in_id)"/>
-    <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text)"/>
-    <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model)"/>
-    <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time)"/>
-    <expand macro="advanced_options">
-      <param name="param_max_number_of_peptides" type="integer" value="100000" label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)." help="(-max_number_of_peptides)"/>
-      <param name="param_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz true" falsevalue="-out_id:rewrite_peptideidentification_rtmz false" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_file" label="Output file with peptide RT prediction" format="idXML"/>
-    <data name="param_positive" label="Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well." format="idXML"/>
-    <data name="param_negative" label="Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well." format="idXML"/>
-    <data name="param_file" label="Output file with predicted RT values" format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Predicts retention times for peptides using a model trained by RTModel.
+    <inputs>
+      <param format="xml" help="(-in_id) " label="Peptides with precursor information" name="param_in_id" optional="True" type="data"/>
+      <param format="txt" help="(-in_text) " label="Peptides as text-based file" name="param_in_text" optional="True" type="data"/>
+      <param format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by RTModel)" name="param_svm_model" optional="False" type="data"/>
+      <param help="(-total_gradient_time) " label="The time (in seconds) of the gradient (peptide RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
+      <expand macro="advanced_options">
+        <param help="(-max_number_of_peptides) " label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param checked="false" falsevalue="" help="(-rewrite_peptideidentification_rtmz) " label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" name="param_out_id_rewrite_peptideidentification_rtmz" optional="True" truevalue="-out_id:rewrite_peptideidentification_rtmz" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out_id_file"/>
+      <data format="xml" name="param_out_id_positive"/>
+      <data format="xml" name="param_out_id_negative"/>
+      <data format="tabular" name="param_out_text_file"/>
+    </outputs>
+    <help>Predicts retention times for peptides using a model trained by RTModel.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
+  </tool>