--- a/FeatureFinderMetaboIdent.xml	Thu Dec 01 19:09:59 2022 +0000
+++ b/FeatureFinderMetaboIdent.xml	Fri Jun 14 21:30:15 2024 +0000
@@ -1,8 +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 CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects features in MS1 data based on metabolite identifications.</description>
+  <description>Detects features in MS1 data based on metabolite identifications</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir lib_out &&
@@ -25,12 +24,12 @@
 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir chrom_out &&
 #end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir trafo_out &&
+#end if
 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir candidates_out &&
 #end if
-#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir trafo_out &&
-#end if
 
 ## Main program call
 
@@ -52,14 +51,14 @@
   -chrom_out
   'chrom_out/output.${gxy2omsext("mzml")}'
 #end if
-#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -candidates_out
-  'candidates_out/output.${gxy2omsext("featurexml")}'
-#end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
   'trafo_out/output.${gxy2omsext("trafoxml")}'
 #end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -candidates_out
+  'candidates_out/output.${gxy2omsext("txt")}'
+#end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -72,12 +71,12 @@
 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
 #end if
-#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
-#end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
 #end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'candidates_out/output.${gxy2omsext("txt")}' '$candidates_out'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -86,52 +85,52 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="tabular" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
     <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
-      <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
-      <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
-      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
-      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
+      <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
+      <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
+      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
+      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
     </section>
     <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
-      <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
-      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
-      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
+      <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
+      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
+      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
     </section>
     <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
         <option value="symmetric" selected="true">symmetric</option>
         <option value="asymmetric">asymmetric</option>
         <option value="none">none</option>
         <expand macro="list_string_san" name="type"/>
       </param>
-      <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
+      <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
       <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
       <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" 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=""/>
       <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
       <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
-        <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
-        <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" 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=""/>
-        <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
-        <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
+        <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" 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=""/>
+        <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
       </section>
     </section>
     <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
-      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
+      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
       <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
       <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
       <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
-      <option value="candidates_out_FLAG">candidates_out (Optional output file with feature candidates)</option>
       <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
+      <option value="candidates_out_FLAG">candidates_out (Optional output file: Feature candidates (before filtering and model fitting))</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -143,17 +142,18 @@
     <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
       <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
-    <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
     <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="txt">
+      <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_FeatureFinderMetaboIdent_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMetaboIdent_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -161,7 +161,7 @@
       </section>
       <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
       <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="extract">
         <param name="mz_window" value="5.0"/>
         <param name="rt_window" value="20.0"/>
@@ -196,11 +196,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetaboIdent.html]]></help>
   <expand macro="references"/>
 </tool>