--- a/FeatureFinderIdentification.xml	Thu Apr 27 13:19:43 2017 -0400
+++ b/FeatureFinderIdentification.xml	Wed Aug 09 09:54:55 2017 -0400
@@ -1,7 +1,7 @@
 <?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: [Quantitation]-->
-<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0">
+<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.2.0">
   <description>Detects features in MS1 data based on peptide identifications.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
@@ -18,6 +18,9 @@
 #if $param_id:
   -id $param_id
 #end if
+#if $param_id_ext:
+  -id_ext $param_id_ext
+#end if
 #if $param_out:
   -out $param_out
 #end if
@@ -27,29 +30,63 @@
 #if $param_chrom_out:
   -chrom_out $param_chrom_out
 #end if
-#if $param_trafo_out:
-  -trafo_out $param_trafo_out
-#end if
-#if $param_extract_reference_rt:
-  -extract:reference_rt
-  #if " " in str($param_extract_reference_rt):
-    "$param_extract_reference_rt"
-  #else
-    $param_extract_reference_rt
-  #end if
-#end if
-#if $param_extract_rt_window:
-  -extract:rt_window $param_extract_rt_window
+#if $param_candidates_out:
+  -candidates_out $param_candidates_out
 #end if
 #if $param_extract_mz_window:
   -extract:mz_window $param_extract_mz_window
 #end if
-#if $param_extract_isotope_pmin:
-  -extract:isotope_pmin $param_extract_isotope_pmin
+#if $param_extract_n_isotopes:
+  -extract:n_isotopes $param_extract_n_isotopes
 #end if
 #if $param_detect_peak_width:
   -detect:peak_width $param_detect_peak_width
 #end if
+#if $param_detect_mapping_tolerance:
+  -detect:mapping_tolerance $param_detect_mapping_tolerance
+#end if
+#if $param_svm_samples:
+  -svm:samples $param_svm_samples
+#end if
+#if $param_svm_no_selection:
+  -svm:no_selection
+#end if
+#if $param_svm_xval_out:
+  -svm:xval_out $param_svm_xval_out
+#end if
+#if $param_svm_kernel:
+  -svm:kernel
+  #if " " in str($param_svm_kernel):
+    "$param_svm_kernel"
+  #else
+    $param_svm_kernel
+  #end if
+#end if
+#if $param_svm_xval:
+  -svm:xval $param_svm_xval
+#end if
+
+#if $rep_param_svm_log2_C:
+-svm:log2_C
+  #for token in $rep_param_svm_log2_C:
+    #if " " in str(token):
+      "$token.param_svm_log2_C"
+    #else
+      $token.param_svm_log2_C
+    #end if
+  #end for
+#end if
+
+#if $rep_param_svm_log2_gamma:
+-svm:log2_gamma
+  #for token in $rep_param_svm_log2_gamma:
+    #if " " in str(token):
+      "$token.param_svm_log2_gamma"
+    #else
+      $token.param_svm_log2_gamma
+    #end if
+  #end for
+#end if
 #if $param_model_type:
   -model:type
   #if " " in str($param_model_type):
@@ -59,11 +96,41 @@
   #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_candidates_in:
+  -candidates_in $adv_opts.param_candidates_in
+#end if
     #if $adv_opts.param_force:
   -force
 #end if
-    #if $adv_opts.param_detect_all_features:
-  -detect:all_features
+    #if $adv_opts.param_extract_isotope_pmin:
+  -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin
+#end if
+    #if $adv_opts.param_extract_rt_quantile:
+  -extract:rt_quantile $adv_opts.param_extract_rt_quantile
+#end if
+    #if $adv_opts.param_extract_rt_window:
+  -extract:rt_window $adv_opts.param_extract_rt_window
+#end if
+    #if $adv_opts.param_detect_min_peak_width:
+  -detect:min_peak_width $adv_opts.param_detect_min_peak_width
+#end if
+    #if $adv_opts.param_detect_signal_to_noise:
+  -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise
+#end if
+    #if $adv_opts.param_svm_epsilon:
+  -svm:epsilon $adv_opts.param_svm_epsilon
+#end if
+    #if $adv_opts.param_svm_cache_size:
+  -svm:cache_size $adv_opts.param_svm_cache_size
+#end if
+    #if $adv_opts.param_svm_no_shrinking:
+  -svm:no_shrinking
+#end if
+    #if $adv_opts.param_svm_predictors:
+  -svm:predictors     "$adv_opts.param_svm_predictors"
+#end if
+    #if $adv_opts.param_svm_min_prob:
+  -svm:min_prob $adv_opts.param_svm_min_prob
 #end if
     #if $adv_opts.param_model_add_zeros:
   -model:add_zeros $adv_opts.param_model_add_zeros
@@ -74,6 +141,9 @@
     #if $adv_opts.param_model_no_imputation:
   -model:no_imputation
 #end if
+    #if $adv_opts.param_model_check_min_area:
+  -model:check:min_area $adv_opts.param_model_check_min_area
+#end if
     #if $adv_opts.param_model_check_boundaries:
   -model:check:boundaries $adv_opts.param_model_check_boundaries
 #end if
@@ -86,30 +156,69 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzml" optional="False" label="Input file (LC-MS raw data)" help="(-in) "/>
-    <param name="param_id" type="data" format="idxml" optional="False" label="Input file (peptide identifications)" help="(-id) "/>
-    <param name="param_extract_reference_rt" type="select" optional="False" value="adapt" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge" help="(-reference_rt) 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results)">
-      <option value="adapt" selected="true">adapt</option>
-      <option value="score">score</option>
-      <option value="intensity">intensity</option>
-      <option value="median">median</option>
-      <option value="all">all</option>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Input file: LC-MS raw data" help="(-in) "/>
+    <param name="param_id" type="data" format="idxml" optional="False" label="Input file: Peptide identifications derived directly from 'in'" help="(-id) "/>
+    <param name="param_id_ext" type="data" format="idxml" optional="True" label="Input file: 'External' peptide identifications (" help="(-id_ext) e.g. from aligned runs)"/>
+    <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
+    <param name="param_extract_n_isotopes" type="integer" min="2" optional="True" value="2" label="Number of isotopes to include in each peptide assay" help="(-n_isotopes) "/>
+    <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="(-peak_width) Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
+    <param name="param_detect_mapping_tolerance" type="float" min="0.0" optional="True" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="(-mapping_tolerance) Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
+    <param name="param_svm_samples" type="integer" min="0" optional="True" value="0" label="Number of observations to use for training ('0' for all)" help="(-samples) "/>
+    <param name="param_svm_no_selection" display="radio" type="boolean" truevalue="-svm:no_selection" falsevalue="" checked="false" optional="True" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="(-no_selection) This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
+    <param name="param_svm_kernel" display="radio" type="select" optional="False" value="RBF" label="SVM kernel" help="(-kernel) ">
+      <option value="RBF" selected="true">RBF</option>
+      <option value="linear">linear</option>
     </param>
-    <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="60.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) "/>
-    <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
-    <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.03" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) "/>
-    <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="30.0" label="Elution peak width in seconds for smoothing (Gauss filter)" help="(-peak_width) "/>
+    <param name="param_svm_xval" type="integer" min="1" optional="True" value="5" label="Number of partitions for cross-validation (parameter optimization)" help="(-xval) "/>
+    <repeat name="rep_param_svm_log2_C" min="0" max="1" title="param_svm_log2_C">
+      <param name="param_svm_log2_C" type="text" size="30" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="(-log2_C) A value 'x' is used as 'C = 2^x'">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <repeat name="rep_param_svm_log2_gamma" min="0" max="1" title="param_svm_log2_gamma">
+      <param name="param_svm_log2_gamma" type="text" size="30" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="(-log2_gamma) A value 'x' is used as 'gamma = 2^x'">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
       <option value="symmetric" selected="true">symmetric</option>
       <option value="asymmetric">asymmetric</option>
       <option value="none">none</option>
     </param>
     <expand macro="advanced_options">
+      <param name="param_candidates_in" type="data" format="featurexml" optional="True" label="Input file: Feature candidates from a previous run" help="(-candidates_in) If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored"/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-      <param name="param_detect_all_features" display="radio" type="boolean" truevalue="-detect:all_features" falsevalue="" checked="false" optional="True" label="Return all features detected by OpenSWATH for an assay, instead of only the best one" help="(-all_features) (This requires further processing of the results.)"/>
+      <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) If set, this parameter takes precedence over 'extract:n_isotopes'"/>
+      <param name="param_extract_rt_quantile" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help="(-rt_quantile) "/>
+      <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) If set, this parameter takes precedence over 'extract:rt_quantile'"/>
+      <param name="param_detect_min_peak_width" type="float" min="0.0" optional="True" value="0.2" label="Minimum elution peak width" help="(-min_peak_width) Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
+      <param name="param_detect_signal_to_noise" type="float" min="0.1" optional="True" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help="(-signal_to_noise) "/>
+      <param name="param_svm_epsilon" type="float" min="0.0" optional="True" value="0.001" label="Stopping criterion" help="(-epsilon) "/>
+      <param name="param_svm_cache_size" type="float" min="1.0" optional="True" value="100.0" label="Size of the kernel cache (in MB)" help="(-cache_size) "/>
+      <param name="param_svm_no_shrinking" display="radio" type="boolean" truevalue="-svm:no_shrinking" falsevalue="" checked="false" optional="True" label="Disable the shrinking heuristics" help="(-no_shrinking) "/>
+      <param name="param_svm_predictors" type="text" size="30" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="(-predictors) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_svm_min_prob" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help="(-min_prob) "/>
       <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
       <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
       <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
+      <param name="param_model_check_min_area" type="float" min="0.0" optional="True" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help="(-min_area) "/>
       <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
       <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
       <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
@@ -119,7 +228,8 @@
     <data name="param_out" format="featurexml"/>
     <data name="param_lib_out" format="traml"/>
     <data name="param_chrom_out" format="mzml"/>
-    <data name="param_trafo_out" format="trafoxml"/>
+    <data name="param_candidates_out" format="featurexml"/>
+    <data name="param_svm_xval_out" format="tabular"/>
   </outputs>
   <help>Detects features in MS1 data based on peptide identifications.