--- a/PercolatorAdapter.xml	Thu Sep 24 12:29:50 2020 +0000
+++ b/PercolatorAdapter.xml	Tue Oct 13 20:29:32 2020 +0000
@@ -32,6 +32,18 @@
 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_pin &&
 #end if
+#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pout_target &&
+#end if
+#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pout_decoy &&
+#end if
+#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pout_target_proteins &&
+#end if
+#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pout_decoy_proteins &&
+#end if
 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir weights &&
 #end if
@@ -70,13 +82,29 @@
   -out_pin
   'out_pin/output.${gxy2omsext("tabular")}'
 #end if
+#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pout_target
+  'out_pout_target/output.${gxy2omsext("tabular")}'
+#end if
+#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pout_decoy
+  'out_pout_decoy/output.${gxy2omsext("tabular")}'
+#end if
+#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pout_target_proteins
+  'out_pout_target_proteins/output.${gxy2omsext("tabular")}'
+#end if
+#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pout_decoy_proteins
+  'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}'
+#end if
 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -weights
-  'weights/output.${gxy2omsext("txt")}'
+  'weights/output.${gxy2omsext("tabular")}'
 #end if
 #if $adv_opts_cond.adv_opts_selector=='advanced':
   #if $adv_opts_cond.init_weights:
-    -init-weights
+    -init_weights
     'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)'
   #end if
   #if $adv_opts_cond.fasta:
@@ -93,8 +121,20 @@
 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin'
 #end if
+#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pout_target/output.${gxy2omsext("tabular")}' '$out_pout_target'
+#end if
+#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pout_decoy/output.${gxy2omsext("tabular")}' '$out_pout_decoy'
+#end if
+#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pout_target_proteins/output.${gxy2omsext("tabular")}' '$out_pout_target_proteins'
+#end if
+#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}' '$out_pout_decoy_proteins'
+#end if
 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'weights/output.${gxy2omsext("txt")}' '$weights'
+  && mv 'weights/output.${gxy2omsext("tabular")}' '$weights'
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -129,8 +169,8 @@
       <option value="trypsinp">trypsinp</option>
       <expand macro="list_string_san"/>
     </param>
-    <param name="peptide_level_fdrs" argument="-peptide-level-fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
-    <param name="protein_level_fdrs" argument="-protein-level-fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy-pattern to set the Fasta file and decoy pattern"/>
+    <param name="peptide_level_fdrs" argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
+    <param name="protein_level_fdrs" argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/>
     <param name="osw_level" argument="-osw_level" type="text" optional="true" value="ms2" label="OSW: Either &quot;ms1&quot;, &quot;ms2&quot; or &quot;transition&quot;; the data level selected for scoring" help="">
       <expand macro="list_string_san"/>
     </param>
@@ -141,42 +181,48 @@
       <expand macro="list_string_san"/>
     </param>
     <expand macro="adv_opts_macro">
-      <param name="generic_feature_set" argument="-generic-feature-set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
-      <param name="subset_max_train" argument="-subset-max-train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
+      <param name="generic_feature_set" argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
+      <param name="subset_max_train" argument="-subset_max_train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
       <param name="cpos" argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/>
       <param name="cneg" argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
       <param name="testFDR" argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
       <param name="trainFDR" argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
       <param name="maxiter" argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/>
-      <param name="quick_validation" argument="-quick-validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
-      <param name="init_weights" argument="-init-weights" type="data" format="txt" optional="true" label="Read initial weights to the given file" help=" select txt data sets(s)"/>
-      <param name="default_direction" argument="-default-direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="">
+      <param name="nested_xval_bins" argument="-nested_xval_bins" type="integer" optional="true" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
+      <param name="quick_validation" argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
+      <param name="init_weights" argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/>
+      <param name="static" argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/>
+      <param name="default_direction" argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="">
         <expand macro="list_string_san"/>
       </param>
       <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
       <param name="unitnorm" argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/>
-      <param name="test_each_iteration" argument="-test-each-iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/>
+      <param name="test_each_iteration" argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/>
       <param name="override" argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/>
       <param name="seed" argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/>
       <param name="doc" argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/>
       <param name="klammer" argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/>
-      <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein-level-fdrs is active)" help=" select fasta data sets(s)"/>
-      <param name="decoy_pattern" argument="-decoy-pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein-level-fdrs is active)" help="">
+      <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/>
+      <param name="decoy_pattern" argument="-decoy_pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help="">
         <expand macro="list_string_san"/>
       </param>
-      <param name="post_processing_tdc" argument="-post-processing-tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/>
-      <param name="train_best_positive" argument="-train-best-positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/>
+      <param name="post_processing_tdc" argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/>
+      <param name="train_best_positive" argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/>
       <param name="ipf_max_peakgroup_pep" argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/>
       <param name="ipf_max_transition_isotope_overlap" argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
       <param name="ipf_min_transition_sn" argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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="out_pin_FLAG">out_pin (Enables the test mode (needed for internal use only))</option>
-      <option value="weights_FLAG">weights (Enables the test mode (needed for internal use only))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option>
+      <option value="out_pout_target_FLAG">out_pout_target (Write pout file (e.g., for debugging))</option>
+      <option value="out_pout_decoy_FLAG">out_pout_decoy (Write pout file (e.g., for debugging))</option>
+      <option value="out_pout_target_proteins_FLAG">out_pout_target_proteins (Write pout file (e.g., for debugging))</option>
+      <option value="out_pout_decoy_proteins_FLAG">out_pout_decoy_proteins (Write pout file (e.g., for debugging))</option>
+      <option value="weights_FLAG">weights (Output final weights to the given file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -191,7 +237,19 @@
     <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular">
       <filter>OPTIONAL_OUTPUTS is not None and "out_pin_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
-    <data name="weights" label="${tool.name} on ${on_string}: weights" format="txt">
+    <data name="out_pout_target" label="${tool.name} on ${on_string}: out_pout_target" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_pout_decoy" label="${tool.name} on ${on_string}: out_pout_decoy" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_pout_target_proteins" label="${tool.name} on ${on_string}: out_pout_target_proteins" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_proteins_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_pout_decoy_proteins" label="${tool.name} on ${on_string}: out_pout_decoy_proteins" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_proteins_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="weights" label="${tool.name} on ${on_string}: weights" format="tabular">
       <filter>OPTIONAL_OUTPUTS is not None and "weights_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
@@ -205,6 +263,6 @@
   <help><![CDATA[Facilitate input to Percolator and reintegrate.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_PercolatorAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PercolatorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>