--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDPosteriorErrorProbability.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,85 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDPosteriorErrorProbability
+
+#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':
+    #if $adv_opts.param_smallest_e_value:
+  -smallest_e_value $adv_opts.param_smallest_e_value
+#end if
+    #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 $adv_opts.param_fit_algorithm_incorrectly_assigned:
+  -fit_algorithm:incorrectly_assigned
+  #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
+    "$adv_opts.param_fit_algorithm_incorrectly_assigned"
+  #else
+    $adv_opts.param_fit_algorithm_incorrectly_assigned
+  #end if
+#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" falsevalue="" checked="false" optional="True" label="The search engine scores are split by charge if this flag is set" help="(-split_charge) Thus, for each charge state a new model will be computed"/>
+    <param name="param_top_hits_only" type="boolean" truevalue="-top_hits_only" falsevalue="" 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" falsevalue="" checked="false" optional="True" label="If set errors will be written but ignored" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
+    <param name="param_prob_correct" type="boolean" truevalue="-prob_correct" falsevalue="" 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" help="(-smallest_e_value) It should not be 0, as transformation in a real number (log of E-value) is not possible for certain values then"/>
+      <param name="param_fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" 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"/>
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_fit_algorithm_number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized"/>
+      <param name="param_fit_algorithm_incorrectly_assigned" type="select" optional="True" value="Gumbel" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used">
+        <option value="Gumbel">Gumbel</option>
+        <option value="Gauss">Gauss</option>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+    <data name="param_out_plot" 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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
+  <expand macro="references"/>
+</tool>