--- a/IDPosteriorErrorProbability.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDPosteriorErrorProbability.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,56 +1,85 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="1.12.0">
-  <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDPosteriorErrorProbability
+<?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: [ID Processing]-->
+  <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.0.0">
+    <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDPosteriorErrorProbability
 
--in ${param_in}
--out ${param_out}
--out_plot ${param_out_plot}
-${param_split_charge}
-${param_top_hits_only}
-${param_ignore_bad_data}
-${param_prob_correct}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_plot:
+  -out_plot $param_out_plot
+#end if
+#if $param_split_charge:
+  -split_charge
+#end if
+#if $param_top_hits_only:
+  -top_hits_only
+#end if
+#if $param_ignore_bad_data:
+  -ignore_bad_data
+#end if
+#if $param_prob_correct:
+  -prob_correct
+#end if
+-threads \${GALAXY_SLOTS:-24}
 #if $adv_opts.adv_opts_selector=='advanced':
-    -smallest_e_value ${adv_opts.param_smallest_e_value}
-    -fdr_for_targets_smaller ${adv_opts.param_fdr_for_targets_smaller}
-    -fit_algorithm:number_of_bins ${adv_opts.param_number_of_bins}
-    -fit_algorithm:incorrectly_assigned ${adv_opts.param_incorrectly_assigned}
+    #if $adv_opts.param_fdr_for_targets_smaller:
+  -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_fit_algorithm_number_of_bins:
+  -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
+#end if
+    #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
+  -fit_algorithm:incorrectly_assigned
+  #if &quot; &quot; in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
+    &quot;$adv_opts.param_fit_algorithm_incorrectly_assigned&quot;
+  #else
+    $adv_opts.param_fit_algorithm_incorrectly_assigned
+  #end if
+#end if
+    #if $adv_opts.param_fit_algorithm_max_nr_iterations:
+  -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="idXML" optional="False" label="input file " help="(-in)"/>
-    <param name="param_split_charge" type="boolean" truevalue="-split_charge true" falsevalue="-split_charge false" checked="false" optional="True" label="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." help="(-split_charge)"/>
-    <param name="param_top_hits_only" type="boolean" truevalue="-top_hits_only true" falsevalue="-top_hits_only false" checked="false" optional="True" label="If set only the top hits of every PeptideIdentification will be used" help="(-top_hits_only)"/>
-    <param name="param_ignore_bad_data" type="boolean" truevalue="-ignore_bad_data true" falsevalue="-ignore_bad_data false" checked="false" optional="True" label="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." help="(-ignore_bad_data)"/>
-    <param name="param_prob_correct" type="boolean" truevalue="-prob_correct true" falsevalue="-prob_correct false" checked="false" optional="True" label="If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications." help="(-prob_correct)"/>
-    <expand macro="advanced_options">
-      <param name="param_smallest_e_value" type="float" value="1e-19" label="This value gives a lower bound to E-Values. It should not be 0, as transformation in a real number (log of E-value) is not possible for certain values then." help="(-smallest_e_value)"/>
-      <param name="param_fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." help="(-fdr_for_targets_smaller)"/>
-      <param name="param_number_of_bins" type="integer" value="100" label="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" help="(-number_of_bins)"/>
-      <param name="param_incorrectly_assigned" type="select" optional="True" value="Gumbel" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." help="(-incorrectly_assigned)">
-        <option value="Gumbel">Gumbel</option>
-        <option value="Gauss">Gauss</option>
-      </param>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file " format="idXML"/>
-    <data name="param_out_plot" label="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" format="txt"/>
-  </outputs>
-  <help>**What it does**
-
-Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-split_charge) Thus, for each charge state a new model will be computed" label="The search engine scores are split by charge if this flag is set" name="param_split_charge" optional="True" truevalue="-split_charge" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-top_hits_only) " label="If set only the top hits of every PeptideIdentification will be used" name="param_top_hits_only" optional="True" truevalue="-top_hits_only" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through" label="If set errors will be written but ignored" name="param_ignore_bad_data" optional="True" truevalue="-ignore_bad_data" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-prob_correct) " label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" name="param_prob_correct" optional="True" truevalue="-prob_correct" type="boolean"/>
+      <expand macro="advanced_options">
+        <param help="(-fdr_for_targets_smaller) Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run" label="Only used, when top_hits_only set" name="param_fdr_for_targets_smaller" type="float" value="0.05"/>
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized" label="Number of bins used for visualization" name="param_fit_algorithm_number_of_bins" type="integer" value="100"/>
+        <param help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" name="param_fit_algorithm_incorrectly_assigned" optional="True" type="select" value="Gumbel">
+          <option value="Gumbel">Gumbel</option>
+          <option value="Gauss">Gauss</option>
+        </param>
+        <param help="(-max_nr_iterations) " label="Bounds the number of iterations for the EM algorithm when convergence is slow" name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+      <data format="txt" name="param_out_plot"/>
+    </outputs>
+    <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
+  </tool>