--- a/PTModel.xml	Fri May 17 10:24:30 2019 -0400
+++ b/PTModel.xml	Thu Sep 03 16:19:44 2020 +0000
@@ -1,170 +1,114 @@
 <?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 CTDConverter.-->
 <!--Proposed Tool Section: [Peptide property prediction]-->
-<tool id="PTModel" name="PTModel" version="2.3.0">
+<tool id="PTModel" name="PTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <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>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[PTModel
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in_positive &&
+ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
+mkdir in_negative &&
+ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
+mkdir out &&
+
+## Main program call
 
-#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
-#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 $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in_positive
+'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
+-in_negative
+'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
+-out
+'out/output.${gxy2omsext("txt")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("txt")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <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" display="radio" type="select" optional="False" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) ">
+    <param name="in_positive" argument="-in_positive" type="data" format="idxml" optional="false" label="input file with positive examples" help=" select idxml data sets(s)"/>
+    <param name="in_negative" argument="-in_negative" type="data" format="idxml" optional="false" label="input file with negative examples" help=" select idxml data sets(s)"/>
+    <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
+    <param name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" label="the type of the svm (NU_SVC or C_SVC)" help="">
       <option value="NU_SVC">NU_SVC</option>
       <option value="C_SVC" selected="true">C_SVC</option>
+      <expand macro="list_string_san"/>
     </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" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
+    <param name="nu" argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
+    <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" label="the kernel type of the svm" help="">
       <option value="LINEAR">LINEAR</option>
       <option value="RBF">RBF</option>
       <option value="POLY">POLY</option>
       <option value="OLIGO" selected="true">OLIGO</option>
+      <expand macro="list_string_san"/>
     </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" display="radio" 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" display="radio" 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" display="radio" 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" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="degree" argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
+    <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
+    <param name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
+    <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
+    <param name="max_positive_count" argument="-max_positive_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
+    <param name="max_negative_count" argument="-max_negative_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
+    <param name="redundant" argument="-redundant" type="boolean" truevalue="true" falsevalue="false" checked="false" 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=""/>
+    <param name="additive_cv" argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" 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=""/>
+    <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
+      <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" help=""/>
+      <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="10" label="number of runs for the CV" help=""/>
+      <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
+      <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
+      <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
+      <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
+      <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
+      <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="100.0" label="step size of c" help=""/>
+      <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
+      <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="starting point of nu" help=""/>
+      <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.3" label="step size of nu" help=""/>
+      <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.9" label="stopping point of nu" help=""/>
+      <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
+      <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
+      <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
+    </section>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san"/>
+      </param>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="txt"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Trains a model for the prediction of proteotypic peptides from a training set.
+  <tests>
+    <expand macro="autotest_PTModel"/>
+    <expand macro="manutest_PTModel"/>
+  </tests>
+  <help><![CDATA[Trains a model for the prediction of proteotypic peptides from a training set.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PTModel.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_PTModel.html]]></help>
+  <expand macro="references"/>
 </tool>