--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RTPredict.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>RTPredict
+
+#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':
+    #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_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_out_id_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz" falsevalue="" 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_out_id_file" format="idxml"/>
+    <data name="param_out_id_positive" format="idxml"/>
+    <data name="param_out_id_negative" format="idxml"/>
+    <data name="param_out_text_file" format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+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</help>
+  <expand macro="references"/>
+</tool>