--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PTModel.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,171 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PTModel" name="PTModel" version="2.0.0">
+  <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PTModel</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PTModel
+
+#if $param_in_positive:
+  -in_positive $param_in_positive
+#end if
+#if $param_in_negative:
+  -in_negative $param_in_negative
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_c:
+  -c $param_c
+#end if
+#if $param_svm_type:
+  -svm_type
+  #if " " in str($param_svm_type):
+    "$param_svm_type"
+  #else
+    $param_svm_type
+  #end if
+#end if
+#if $param_nu:
+  -nu $param_nu
+#end if
+#if $param_kernel_type:
+  -kernel_type
+  #if " " in str($param_kernel_type):
+    "$param_kernel_type"
+  #else
+    $param_kernel_type
+  #end if
+#end if
+#if $param_degree:
+  -degree $param_degree
+#end if
+#if $param_border_length:
+  -border_length $param_border_length
+#end if
+#if $param_k_mer_length:
+  -k_mer_length $param_k_mer_length
+#end if
+#if $param_sigma:
+  -sigma $param_sigma
+#end if
+#if $param_max_positive_count:
+  -max_positive_count $param_max_positive_count
+#end if
+#if $param_max_negative_count:
+  -max_negative_count $param_max_negative_count
+#end if
+#if $param_redundant:
+  -redundant
+#end if
+#if $param_additive_cv:
+  -additive_cv
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_cv_skip_cv:
+  -cv:skip_cv
+#end if
+#if $param_cv_number_of_runs:
+  -cv:number_of_runs $param_cv_number_of_runs
+#end if
+#if $param_cv_number_of_partitions:
+  -cv:number_of_partitions $param_cv_number_of_partitions
+#end if
+#if $param_cv_degree_start:
+  -cv:degree_start $param_cv_degree_start
+#end if
+#if $param_cv_degree_step_size:
+  -cv:degree_step_size $param_cv_degree_step_size
+#end if
+#if $param_cv_degree_stop:
+  -cv:degree_stop $param_cv_degree_stop
+#end if
+#if $param_cv_c_start:
+  -cv:c_start $param_cv_c_start
+#end if
+#if $param_cv_c_step_size:
+  -cv:c_step_size $param_cv_c_step_size
+#end if
+#if $param_cv_c_stop:
+  -cv:c_stop $param_cv_c_stop
+#end if
+#if $param_cv_nu_start:
+  -cv:nu_start $param_cv_nu_start
+#end if
+#if $param_cv_nu_step_size:
+  -cv:nu_step_size $param_cv_nu_step_size
+#end if
+#if $param_cv_nu_stop:
+  -cv:nu_stop $param_cv_nu_stop
+#end if
+#if $param_cv_sigma_start:
+  -cv:sigma_start $param_cv_sigma_start
+#end if
+#if $param_cv_sigma_step_size:
+  -cv:sigma_step_size $param_cv_sigma_step_size
+#end if
+#if $param_cv_sigma_stop:
+  -cv:sigma_stop $param_cv_sigma_stop
+#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_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/>
+    <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/>
+    <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
+    <param name="param_svm_type" type="select" optional="True" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) ">
+      <option value="NU_SVC">NU_SVC</option>
+      <option value="C_SVC">C_SVC</option>
+    </param>
+    <param name="param_nu" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help="(-nu) "/>
+    <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
+      <option value="LINEAR">LINEAR</option>
+      <option value="RBF">RBF</option>
+      <option value="POLY">POLY</option>
+      <option value="OLIGO">OLIGO</option>
+    </param>
+    <param name="param_degree" type="integer" min="1" optional="True" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help="(-degree) "/>
+    <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
+    <param name="param_k_mer_length" type="integer" min="1" optional="True" value="1" label="k_mer length of the POBK" help="(-k_mer_length) "/>
+    <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
+    <param name="param_max_positive_count" type="integer" min="1" optional="True" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help="(-max_positive_count) "/>
+    <param name="param_max_negative_count" type="integer" min="1" optional="True" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help="(-max_negative_count) "/>
+    <param name="param_redundant" type="boolean" truevalue="-redundant" falsevalue="" checked="false" optional="True" label="if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set" help="(-redundant) "/>
+    <param name="param_additive_cv" type="boolean" truevalue="-additive_cv" falsevalue="" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value" help="(-additive_cv) "/>
+    <param name="param_cv_skip_cv" type="boolean" truevalue="-cv:skip_cv" falsevalue="" checked="false" optional="True" label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" help="(-skip_cv) "/>
+    <param name="param_cv_number_of_runs" type="integer" min="1" optional="True" value="10" label="number of runs for the CV" help="(-number_of_runs) "/>
+    <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
+    <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
+    <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
+    <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
+    <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
+    <param name="param_cv_c_step_size" type="float" value="100.0" label="step size of c" help="(-c_step_size) "/>
+    <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
+    <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="starting point of nu" help="(-nu_start) "/>
+    <param name="param_cv_nu_step_size" type="float" value="1.3" label="step size of nu" help="(-nu_step_size) "/>
+    <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.9" label="stopping point of nu" help="(-nu_stop) "/>
+    <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
+    <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
+    <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
+    <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**
+
+Trains a model for the prediction of proteotypic peptides from a training set.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help>
+  <expand macro="references"/>
+</tool>