Mercurial > repos > galaxyp > openms_featurefinderidentification

changeset 16:65bdfab68571 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:29 +0000
parents 5dc928c83939
children
files FeatureFinderIdentification.xml fill_ctd_clargs.py generate-foo.sh get_tests.py macros.xml prepare_test_data_manual.sh readme.md test-data.sh
diffstat 8 files changed, 505 insertions(+), 431 deletions(-) [+]
line wrap: on
line diff
--- a/FeatureFinderIdentification.xml	Thu Dec 01 19:24:30 2022 +0000
+++ b/FeatureFinderIdentification.xml	Fri Jun 14 21:44:29 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: [Quantitation]-->
 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects features in MS1 data based on peptide identifications.</description>
+  <description>Detects features in MS1 data based on peptide identifications</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
     <import>macros.xml</import>
@@ -15,12 +14,12 @@
 
 ## 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)' &&
 #if $id_ext:
   mkdir id_ext &&
-  ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
+  cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
 #end if
 mkdir out &&
 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -35,11 +34,13 @@
 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir svm_xval_out &&
 #end if
+## advanced options
   #if $adv_opts.candidates_in:
     mkdir adv_opts.candidates_in &&
-    ln -s '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
+    cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -72,10 +73,12 @@
   -svm:xval_out
   'svm_xval_out/output.${gxy2omsext("csv")}'
 #end if
+## advanced options
   #if $adv_opts.candidates_in:
     -candidates_in
     'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -102,73 +105,80 @@
     <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="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml 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="idxml" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
     <param argument="-id_ext" type="data" format="idxml" optional="true" label="Input file: 'External' peptide identifications" help="(e.g. from aligned runs) select idxml data sets(s)"/>
     <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/>
+    <param argument="-min_psm_cutoff" type="text" value="none" label="Minimum score for the best PSM of a spectrum to be used as seed" help="Use 'none' for no cutoff">
+      <expand macro="list_string_san" name="min_psm_cutoff"/>
+    </param>
+    <param argument="-add_mass_offset_peptides" type="float" min="0.0" value="0.0" label="If for every peptide (or seed) also an offset peptide is extracted (true)" help="Can be used to downstream to determine MBR false transfer rates. (0.0 = disabled)"/>
     <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
-      <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
-      <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="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="rt_quantile" argument="-extract:rt_quantile" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" 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="batch_size" argument="-extract:batch_size" type="integer" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
+      <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="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'"/>
+      <param name="rt_quantile" argument="-extract:rt_quantile" type="float" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" 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'"/>
     </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="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" optional="true" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
+      <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=""/>
+      <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
     </section>
     <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
-      <param name="samples" argument="-svm:samples" type="integer" optional="true" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
+      <param name="samples" argument="-svm:samples" type="integer" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
       <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="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="kernel" argument="-svm:kernel" type="select" optional="true" label="SVM kernel" help="">
+      <param name="kernel" argument="-svm:kernel" type="select" label="SVM kernel" help="">
         <option value="RBF" selected="true">RBF</option>
         <option value="linear">linear</option>
         <expand macro="list_string_san" name="kernel"/>
       </param>
-      <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
-      <param name="log2_C" argument="-svm:log2_C" type="text" optional="true" 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="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="xval" argument="-svm:xval" type="integer" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
+      <param name="log2_C" argument="-svm:log2_C" type="text" 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="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="log2_C"/>
       </param>
-      <param name="log2_gamma" argument="-svm:log2_gamma" type="text" optional="true" 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="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="log2_gamma" argument="-svm:log2_gamma" type="text" 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="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="log2_gamma"/>
       </param>
-      <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/>
-      <param name="cache_size" argument="-svm:cache_size" type="float" optional="true" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
+      <param name="log2_p" argument="-svm:log2_p" type="text" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0" label="Values to try for the SVM parameter 'epsilon' during parameter optimization (epsilon-SVR only)" help="A value 'x' is used as 'epsilon = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <expand macro="list_float_valsan" name="log2_p"/>
+      </param>
+      <param name="epsilon" argument="-svm:epsilon" type="float" min="0.0" value="0.001" label="Stopping criterion" help=""/>
+      <param name="cache_size" argument="-svm:cache_size" type="float" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
       <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/>
-      <param name="predictors" argument="-svm:predictors" type="text" optional="true" 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_ms1_isotope_correlation_score,var_ms1_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="">
+      <param name="predictors" argument="-svm:predictors" type="text" 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_ms1_isotope_correlation_score,var_ms1_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="">
         <expand macro="list_string_san" name="predictors"/>
       </param>
-      <param name="min_prob" argument="-svm:min_prob" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
+      <param name="min_prob" argument="-svm:min_prob" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" 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="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/>
       <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>
@@ -198,7 +208,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderIdentification_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderIdentification_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -206,8 +217,10 @@
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="5000"/>
         <param name="mz_window" value="0.1"/>
@@ -229,6 +242,7 @@
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -258,6 +272,9 @@
           <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>
     <!-- TOPP_FeatureFinderIdentification_3 -->
     <test expect_num_outputs="2">
@@ -267,8 +284,10 @@
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_3.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="5000"/>
         <param name="mz_window" value="0.1"/>
@@ -290,6 +309,7 @@
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -319,6 +339,9 @@
           <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>
     <!-- TOPP_FeatureFinderIdentification_5 -->
     <test expect_num_outputs="3">
@@ -328,9 +351,11 @@
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_5.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="candidates_out" file="FeatureFinderIdentification_5_candidates.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="candidates_out" value="FeatureFinderIdentification_5_candidates.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="10"/>
         <param name="mz_window" value="0.1"/>
@@ -352,6 +377,7 @@
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -381,11 +407,14 @@
           <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 peptide identifications.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIdentification.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIdentification.html]]></help>
   <expand macro="references"/>
 </tool>
--- a/fill_ctd_clargs.py	Thu Dec 01 19:24:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/env python3
-
-import operator
-from argparse import ArgumentParser
-from functools import reduce  # forward compatibility for Python 3
-from io import StringIO
-
-from CTDopts.CTDopts import (
-    _Null,
-    CTDModel,
-    ModelTypeError,
-    Parameters
-)
-
-
-def getFromDict(dataDict, mapList):
-    return reduce(operator.getitem, mapList, dataDict)
-
-
-def setInDict(dataDict, mapList, value):
-    getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
-
-
-if __name__ == "__main__":
-    # note add_help=False since otherwise arguments starting with -h will
-    # trigger an error (despite allow_abbreviate)
-    parser = ArgumentParser(prog="fill_ctd_clargs",
-                            description="fill command line arguments"
-                            "into a CTD file and write the CTD file to stdout",
-                            add_help=False, allow_abbrev=False)
-    parser.add_argument("--ini_file", dest="ini_file", help="input ini file",
-                        metavar='INI', default=None, required=True)
-    parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file"
-                        "if given then optional parameters from the ini file"
-                        "will be filled with the defaults from this CTD file",
-                        metavar='CTD', default=None, required=False)
-    args, cliargs = parser.parse_known_args()
-
-    # load CTDModel
-    ini_model = None
-    try:
-        ini_model = CTDModel(from_file=args.ini_file)
-    except ModelTypeError:
-        pass
-    try:
-        ini_model = Parameters(from_file=args.ini_file)
-    except ModelTypeError:
-        pass
-    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file)
-
-    # get a dictionary of the ctd arguments where the values of the parameters
-    # given on the command line are overwritten
-    ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
-
-    if args.ctd_file:
-        ctd_model = CTDModel(from_file=args.ctd_file)
-        ctd_values = ctd_model.get_defaults()
-        for param in ini_model.get_parameters():
-            if not param.required and (param.default is None or type(param.default) is _Null):
-                lineage = param.get_lineage(name_only=True)
-                try:
-                    default = getFromDict(ctd_values, lineage)
-                except KeyError:
-                    continue
-                setInDict(ini_values, lineage, default)
-
-    # write the ctd with the values taken from the dictionary
-    out = StringIO()
-    ctd_tree = ini_model.write_ctd(out, ini_values)
-    print(out.getvalue())
--- a/generate-foo.sh	Thu Dec 01 19:24:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,215 +0,0 @@
-#!/usr/bin/env bash
-
-# parse test definitions from OpenMS sources for a tool with a given id
-function get_tests2 {
-    id=$1
-    >&2 echo "generate tests for $id"
-    echo '<xml name="autotest_'"$id"'">'
-
-    # get the tests from the CMakeLists.txt
-    # 1st remove some tests
-    # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
-    # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
-    # - several tools with duplicated input (leads to conflict when linking)
-    # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
-    # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
-    # - some input files are originally in a subdir (degenerated cases/), but not in test-data
-    # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-    # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
-    # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
-    CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
-        sed 's@${DATA_DIR_SHARE}/@@g' |
-        grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
-        sed 's/${TMP_RIP_PATH}/""/' |
-        grep -v "MaRaClusterAdapter.*-consensus_out"|
-        grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
-        sed 's@degenerate_cases/@@g' |
-        egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
-        sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
-        grep -v '"TOPP_SiriusAdapter_10"')
-
-    # 1st part is a dirty hack to join lines containing a single function call, e.g.
-    # addtest(....
-    #         ....)
-    echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-        grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE"  | while read -r line
-    do
-        line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
-        # >&2 echo $line
-        test_id=$(echo "$line" | cut -d" " -f 1)
-        tool_id=$(echo "$line" | cut -d" " -f 2)
-        # >&2 echo "test_id $test_id"
-        if [[ $test_id =~ _out_?[0-9]? ]]; then
-            >&2 echo "    skip $test_id $line"
-            continue
-        fi
-        if [[ ${id,,} != ${tool_id,,} ]]; then
-            >&2 echo "    skip $test_id ($id != $tool_id) $line"
-            continue
-        fi
-
-        #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
-        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-            >&2 echo "    skip failing "$test_id
-            continue
-        fi
-        tes="  <test>\n"
-        line=$(fix_tmp_files "$line")
-        line=$(unique_files "$line")
-        # >&2 echo LINE $line
-        #if there is an ini file then we use this to generate the test
-        #otherwise the ctd file is used
-        #other command line parameters are inserted later into this xml
-        if grep -lq "\-ini" <<<"$line"; then
-            ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
-            ini="test-data/$ini"
-        else
-            ini="ctd/$tool_id.ctd"
-        fi
-        # >&2 echo "========================================================"
-        # >&2 echo "USING ini $ini"
-        cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
-
-        ctdtmp=$(mktemp)
-        # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-        # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" 
-        eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp"
-        # >&2 echo $ctdtmp
-        # >&2 cat $ctdtmp
-        testtmp=$(mktemp)
-        # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7"
-        CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null
-        echo "<!-- $test_id -->"
-        cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-
-        rm "$ctdtmp" "$testtmp"
-
-        #> /dev/null
-
-        #rm $testtmp
-    done 
-    echo '</xml>'
-}
-
-#some tests use the same file twice which does not work in planemo tests
-#hence we create symlinks for each file used twice
-function unique_files {
-    line=$@
-    for arg in $@
-    do
-        if [[ ! -f "test-data/$arg" ]]; then
-            continue
-        fi
-        cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-        while [[ $cnt -gt 1 ]]; do
-            new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./")
-            ln -fs $arg test-data/$new_arg
-            line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
-            cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-        done
-    done
-
-    echo $line
-}
-
-# options of out_type selects need to be fixed to Galaxy data types
-function fix_out_type {
-    grep "^$1" "$2" | awk '{print $2}'
-}
-
-#OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
-#problem: the extension of the tmp files is unusable for test generation.
-#unfortunately the extensions used in the DIFF lines are not always usable for the CLI
-#(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
-#this function replaces the tmp file by the expected file. 
-function fix_tmp_files {
-    # >&2 echo "FIX $line"
-    ret=""
-    for a in $@; do
-        # >&2 echo "    a "$a
-        if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
-            ret="$ret $a"
-            continue
-        fi
-        diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
-        # >&2 echo "    diff_line "$diff_line
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line)
-        # >&2 echo "    in1 "$in1
-        if [[  "$a" != "$in1" ]]; then
-            ret="$ret $a"
-            continue
-        fi
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line)
-        in2=$(basename $in2 | sed 's/)$//')
-        # >&2 echo "    in2 "$in2
-        if [[ -f "test-data/$in2" ]]; then
-            ln -fs "$in1" "test-data/$in2"
-            ret="$ret $in2"
-        else
-            ret="$ret $a"
-        fi
-    done
-#    >&2 echo "--> $ret"
-    echo "$ret"
-}
-
-function link_tmp_files {
-    # note this also considers commented lines (starting with a #)
-    # because of tests where the diff command is commented and we
-    # still want to use the extension of these files
-    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line
-    do
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line)
-        in1=$(basename $in1 | sed 's/)$//')
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line)
-        in2=$(basename $in2 | sed 's/)$//')
-        if [[ "$in1" == "$in2" ]]; then
-            >&2 echo "not linking equal $in1 $in2"
-            continue
-        fi
-        ln -f -s $in1 test-data/$in2
-    done
-    
-    find test-data/ -name "*.tmp" -print0 | 
-    while IFS= read -r -d '' i; do 
-        if [ ! -e test-data/$(basename $i .tmp) ]; then
-            ln -s $(basename $i) test-data/$(basename $i .tmp)
-        else
-            ln -fs $(basename $i) test-data/$(basename $i .tmp)
-        fi
-    done
-}
-
-
-
-# parse data preparation calls from OpenMS sources for a tool with a given id
-function prepare_test_data {
-#     id=$1
-# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
-
-    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
-    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-        sed 's/degenerate_cases\///' | 
-        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
-        grep add_test | 
-        egrep "TOPP|UTILS" |
-        sed 's@${DATA_DIR_SHARE}/@@g;'|
-        sed 's@${TMP_RIP_PATH}@./@g'|
-        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
-	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
-    while read line
-    do
-        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
-
-        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-            >&2 echo "    skip failing "$test_id
-            continue
-        fi
-
-        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
-        # line="$(fix_tmp_files $line)"
-        echo 'echo executing "'$test_id'"'
-	echo "$line > $test_id.stdout 2> $test_id.stderr"
-        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
-    done
-}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_tests.py	Fri Jun 14 21:44:29 2024 +0000
@@ -0,0 +1,344 @@
+#!/usr/bin/env python
+
+import argparse
+import os.path
+import re
+import shlex
+import sys
+import tempfile
+from typing import (
+    Dict,
+    List,
+    Optional,
+    TextIO,
+    Tuple,
+)
+
+from ctdconverter.common.utils import (
+    ParameterHardcoder,
+    parse_hardcoded_parameters,
+    parse_input_ctds,
+)
+from ctdconverter.galaxy.converter import convert_models
+from CTDopts.CTDopts import (
+    CTDModel,
+    ModelTypeError,
+    Parameters,
+)
+
+SKIP_LIST = [
+    r"_prepare\"",
+    r"_convert",
+    r"WRITEINI",
+    r"WRITECTD",
+    r"INVALIDVALUE",
+    r"\.ini\.json",
+    r"OpenSwathMzMLFileCacher .*-convert_back",  # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
+    r"MaRaClusterAdapter.*-consensus_out",  # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
+    r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ",  # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
+    r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$',  # no  suppert for cached mzML
+    r'TOPP_SiriusAdapter_[0-9]+$',  # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway
+    r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$'  # Skip AssayGeneratorMetabo tests using Sirius  https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools)
+]
+
+
+def get_failing_tests(cmake: List[str]) -> List[str]:
+    failing_tests = []
+    re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)")
+
+    for cmake in args.cmake:
+        with open(cmake) as cmake_fh:
+            for line in cmake_fh:
+                match = re_fail.search(line)
+                if match:
+                    failing_tests.append(match.group(1))
+    return failing_tests
+
+
+def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str:
+    """
+    OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
+    problem: the extension of the tmp files is unusable for test generation.
+    unfortunately the extensions used in the DIFF lines are not always usable for the CLI
+    (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
+    this function replaces the tmp file by the expected file.
+    """
+    cmd = shlex.split(line)
+    for i, e in enumerate(cmd):
+        if e in diff_pairs:
+            dst = os.path.join("test-data", diff_pairs[e])
+            if os.path.exists(dst):
+                os.unlink(dst)
+            sys.stderr.write(f"symlink {e} {dst}\n")
+            os.symlink(e, dst)
+            cmd[i] = diff_pairs[e]
+    return shlex.join(cmd)
+
+
+def get_ini(line: str, tool_id: str) -> Tuple[str, str]:
+    """
+    if there is an ini file then we use this to generate the test
+    otherwise the ctd file is used
+    other command line parameters are inserted later into this xml
+    """
+    cmd = shlex.split(line)
+    ini = None
+    for i, e in enumerate(cmd):
+        if e == "-ini":
+            ini = cmd[i + 1]
+            cmd = cmd[:i] + cmd[i + 2:]
+    if ini:
+        return os.path.join("test-data", ini), shlex.join(cmd)
+    else:
+        return os.path.join("ctd", f"{tool_id}.ctd"), line
+
+
+def unique_files(line: str):
+    """
+    some tests use the same file twice which does not work in planemo tests
+    hence we create symlinks for each file used twice
+    """
+    cmd = shlex.split(line)
+    # print(f"{cmd}")
+    files = {}
+    # determine the list of indexes where each file argument (anything appearing in test-data/) appears
+    for idx, e in enumerate(cmd):
+        p = os.path.join("test-data", e)
+        if not os.path.exists(p) and not os.path.islink(p):
+            continue
+        try:
+            files[e].append(idx)
+        except KeyError:
+            files[e] = [idx]
+    # print(f"{files=}")
+    for f in files:
+        if len(files[f]) < 2:
+            continue
+        for i, idx in enumerate(files[f]):
+            f_parts = f.split(".")
+            f_parts[0] = f"{f_parts[0]}_{i}"
+            new_f = ".".join(f_parts)
+            # if os.path.exists(os.path.join("test-data", new_f)):
+            #     os.unlink(os.path.join("test-data", new_f))
+            sys.stderr.write(
+                f'\tsymlink {os.path.join("test-data", new_f)} {f}\n'
+            )
+            try:
+                os.symlink(f, os.path.join("test-data", new_f))
+            except FileExistsError:
+                pass
+            cmd[idx] = new_f
+    return shlex.join(cmd)
+
+
+def fill_ctd_clargs(ini: str, line: str, ctd_tmp: TextIO) -> None:
+    cmd = shlex.split(line)
+
+    # load CTDModel
+    ini_model = None
+    try:
+        ini_model = CTDModel(from_file=ini)
+    except ModelTypeError:
+        pass
+    try:
+        ini_model = Parameters(from_file=ini)
+    except ModelTypeError:
+        pass
+    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (
+        args.ini_file
+    )
+
+    # get a dictionary of the ctd arguments where the values of the parameters
+    # given on the command line are overwritten
+    ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True)
+    ini_model.write_ctd(ctd_tmp, ini_values)
+
+
+def process_test_line(
+    id: str,
+    line: str,
+    failing_tests: List[str],
+    skip_list: List[str],
+    diff_pairs: Dict[str, str],
+) -> Optional[str]:
+
+    re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)")
+    re_id_out_test = re.compile(r"_out_?[0-9]?")
+
+    # TODO auto extract from  set(OLD_OSW_PARAM ... lin
+    line = line.replace(
+        "${OLD_OSW_PARAM}",
+        " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false",
+    )
+
+    line = line.replace("${TOPP_BIN_PATH}/", "")
+    line = line.replace("${DATA_DIR_TOPP}/", "")
+    line = line.replace("THIRDPARTY/", "")
+    line = line.replace("${DATA_DIR_SHARE}/", "")
+    # IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differently
+    line = line.replace("${TMP_RIP_PATH}/", "")
+    # some input files are originally in a subdir (degenerated cases/), but not in test-data
+    line = line.replace("degenerate_cases/", "")
+    # determine the test and tool ids and remove the 1) add_test("TESTID" 2) trailing )
+    match = re_test_id.match(line)
+    if not match:
+        sys.exit(f"Ill formated test line {line}\n")
+    test_id = match.group(1)
+    tool_id = match.group(2)
+
+    line = f"{match.group(2)} {match.group(3)}"
+
+    if test_id in failing_tests:
+        sys.stderr.write(f"    skip failing {test_id} {line}\n")
+        return
+
+    if id != tool_id:
+        sys.stderr.write(f"    skip {test_id} ({id} != {tool_id}) {line}\n")
+        return
+
+    if re_id_out_test.search(test_id):
+        sys.stderr.write(f"    skip {test_id} {line}\n")
+        return
+
+    for skip in skip_list:
+        if re.search(skip, line):
+            return
+        if re.search(skip, test_id):
+            return
+
+    line = fix_tmp_files(line, diff_pairs)
+    # print(f"fix {line=}")
+    line = unique_files(line)
+    # print(f"unq {line=}")
+    ini, line = get_ini(line, tool_id)
+
+    from dataclasses import dataclass, field
+
+    @dataclass
+    class CTDConverterArgs:
+        input_files: list
+        output_destination: str
+        default_executable_path: Optional[str] = None
+        hardcoded_parameters: Optional[str] = None
+        parameter_hardcoder: Optional[ParameterHardcoder] = None
+        xsd_location: Optional[str] = None
+        formats_file: Optional[str] = None
+        add_to_command_line: str = ""
+        required_tools_file: Optional[str] = None
+        skip_tools_file: Optional[str] = None
+        macros_files: Optional[List[str]] = field(default_factory=list)
+        test_macros_files: Optional[List[str]] = field(default_factory=list)
+        test_macros_prefix: Optional[List[str]] = field(default_factory=list)
+        test_test: bool = False
+        test_only: bool = False
+        test_unsniffable: Optional[List[str]] = field(default_factory=list)
+        test_condition: Optional[List[str]] = ("compare=sim_size", "delta_frac=0.05")
+        tool_version: str = None
+        tool_profile: str = None
+        bump_file: str = None
+
+    # create an ini/ctd file where the values are equal to the arguments from the command line
+    # and transform it to xml
+    test = [f"<!-- {test_id} -->\n"]
+    with tempfile.NamedTemporaryFile(
+        mode="w+", delete_on_close=False
+    ) as ctd_tmp, tempfile.NamedTemporaryFile(
+        mode="w+", delete_on_close=False
+    ) as xml_tmp:
+        fill_ctd_clargs(ini, line, ctd_tmp)
+        ctd_tmp.close()
+        xml_tmp.close()
+        parsed_ctd = parse_input_ctds(None, [ctd_tmp.name], xml_tmp.name, "xml")
+        ctd_args = CTDConverterArgs(
+            input_files=[ctd_tmp.name],
+            output_destination=xml_tmp.name,
+            macros_files=["macros.xml"],
+            skip_tools_file="aux/tools_blacklist.txt",
+            formats_file="aux/filetypes.txt",
+            # tool_conf_destination = "tool.conf",
+            hardcoded_parameters="aux/hardcoded_params.json",
+            tool_version="3.1",
+            test_only=True,
+            test_unsniffable=[
+                "csv",
+                "tsv",
+                "txt",
+                "dta",
+                "dta2d",
+                "edta",
+                "mrm",
+                "splib",
+            ],
+            test_condition=["compare=sim_size", "delta_frac=0.7"],
+        )
+        ctd_args.parameter_hardcoder = parse_hardcoded_parameters(
+            ctd_args.hardcoded_parameters
+        )
+        convert_models(ctd_args, parsed_ctd)
+        xml_tmp = open(xml_tmp.name, "r")
+        for l in xml_tmp:
+            test.append(l)
+
+    return "".join(test)
+
+
+parser = argparse.ArgumentParser(description="Create Galaxy tests for a OpenMS tools")
+parser.add_argument("--id", dest="id", help="tool id")
+parser.add_argument("--cmake", nargs="+", help="OpenMS test CMake files")
+args = parser.parse_args()
+sys.stderr.write(f"generate tests for {args.id}\n")
+
+re_comment = re.compile("#.*")
+re_empty_prefix = re.compile(r"^\s*")
+re_empty_suffix = re.compile(r"\s*$")
+re_add_test = re.compile(r"add_test\(\"(TOPP|UTILS)_.*/" + args.id)
+re_diff = re.compile(r"\$\{DIFF\}.* -in1 ([^ ]+) -in2 ([^ ]+)")
+failing_tests = get_failing_tests(args.cmake)
+tests = []
+
+# process the given CMake files and compile lists of
+# - test lines .. essentially add_test(...)
+# - and pairs of files that are diffed
+jline = ""
+test_lines = []
+diff_pairs = {}
+for cmake in args.cmake:
+    with open(cmake) as cmake_fh:
+        for line in cmake_fh:
+            # remove comments, empty prefixes and suffixes
+            line = re_comment.sub("", line)
+            line = re_empty_prefix.sub("", line)
+            line = re_empty_suffix.sub("", line)
+            # skip empty lines
+            if line == "":
+                continue
+
+            # join test statements that are split over multiple lines
+            if line.endswith(")"):
+                jline += " " + line[:-1]
+            else:
+                jline = line
+                continue
+            line, jline = jline.strip(), ""
+            match = re_diff.search(line)
+            if match:
+                in1 = match.group(1).split("/")[-1]
+                in2 = match.group(2).split("/")[-1]
+                if in1 != in2:
+                    diff_pairs[in1] = in2
+            elif re_add_test.match(line):
+                test_lines.append(line)
+
+for line in test_lines:
+    test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs)
+    if test:
+        tests.append(test)
+
+tests = "\n".join(tests)
+print(
+    f"""
+<xml name="autotest_{args.id}">
+{tests}
+</xml>
+"""
+)
--- a/macros.xml	Thu Dec 01 19:24:30 2022 +0000
+++ b/macros.xml	Fri Jun 14 21:44:29 2024 +0000
@@ -3,19 +3,19 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.8</token>
+  <token name="@TOOL_VERSION@">3.1</token>
   <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@TEST_DATA_LOCATION@"/>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
       <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
-      <requirement type="package" version="2.1.9">omssa</requirement>
-      <requirement type="package" version="2.13.0">blast</requirement>
+      <requirement type="package" version="2.14.1">blast</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
-	  <requirement type="package" version="1.4">ctdopts</requirement>
+	  <requirement type="package" version="1.5">ctdopts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -26,6 +26,8 @@
       <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
       <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
       <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
+      <regex match="OMSSA ran out of RAM" level="fatal_oom" description="Could not allocate memory"/>
+      <regex match="comet' crashed hard (segfault-like). Please check the log." level="fatal_oom" description="Could not allocate memory"/>
     </stdio>
   </xml>
   <xml name="references">
@@ -113,11 +115,11 @@
   </token>
 
 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
-    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
+    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'}
     #return m[o]
 #end def
 #def gxy2omsext(g)
-    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
+    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'}
     #return m[g]
 #end def
 ]]></token></macros>
--- a/prepare_test_data_manual.sh	Thu Dec 01 19:24:30 2022 +0000
+++ b/prepare_test_data_manual.sh	Fri Jun 14 21:44:29 2024 +0000
@@ -1,8 +1,3 @@
-MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
@@ -13,8 +8,7 @@
 CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
+# TODO DeMeanderize
 
 # TODO DigestorMotif
 
@@ -30,26 +24,17 @@
 if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 
-FFEval -test -in  FeatureFinderCentroided_1_output.featureXML -truth  FeatureFinderCentroided_1_output.featureXML -out  FFEval.featureXML -out_roc FFEval_roc.csv  > FFEval.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 # TODO? deprecated IDDecoyProbability
 
 IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides  1 -out  IDExtractor.idXML   > IDExtractor.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-LabeledEval -test -in  FeatureLinkerLabeled_1_input.featureXML -truth  FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
@@ -68,20 +53,6 @@
 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr
 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-# adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719
-FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-#PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ 
-
 # TODO PhosphoScoring 
 PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
@@ -118,9 +89,6 @@
 RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
@@ -152,13 +120,8 @@
 SpectraFilterThresholdMower -test -in  SpectraFilterSqrtMower_1_input.mzML -out  SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr
+SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML -algorithm:average_gaussian:ms_level 2 > SpectraMerger.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-# TODO SvmTheoreticalSpectrumGeneratorTrainer
-
-TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
--- a/readme.md	Thu Dec 01 19:24:30 2022 +0000
+++ b/readme.md	Fri Jun 14 21:44:29 2024 +0000
@@ -11,7 +11,7 @@
  * https://www.openms.de/
 
 The wrappers for these tools and most of their tests are automatically
-generated using the `generate.sh` script. The generation of the tools is
+generated using the `./aux/generate.sh` script. The generation of the tools is
 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter)
 which can be fine tuned via the `hardcoded_params.json` file. This file allows
 to blacklist and hardcode parameters and to modify or set arbitrary
@@ -129,15 +129,6 @@
 Open problems
 =============
 
-Some tools stall in CI testing using `--biocontainers` which is why the OpenMS
-tools are currently listed in `.tt_biocontainer_skip`. This is
-
-- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)
-- OMSSAAdapter
-
-Using `docker -t` seems to solve the problem (see
-https://github.com/galaxyproject/galaxy/issues/10153).
-
 Licence (MIT)
 =============
 
--- a/test-data.sh	Thu Dec 01 19:24:30 2022 +0000
+++ b/test-data.sh	Fri Jun 14 21:44:29 2024 +0000
@@ -1,11 +1,10 @@
 #!/usr/bin/env bash
 
-VERSION=2.8
+# set -x
+
+VERSION=3.1
 FILETYPES="aux/filetypes.txt"
-CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"
-
-# import the magic
-. ./generate-foo.sh
+CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2"
 
 # install conda
 if [ -z "$tmp" ]; then
@@ -45,17 +44,20 @@
 
 echo "Clone OpenMS $VERSION sources"
 if [[ ! -d $OPENMSGIT ]]; then
-    # TODO >2.8 reenable original release branch .. also in else branch
-    # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
-    # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
-    git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
-    cd $OPENMSGIT
-    git submodule init
-    git submodule update
-    cd -
+    if [[ "$created" == "yes" ]]; then
+        GIT_DIR=$(mktemp -d --dry-run)
+        GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR"
+    fi
+    git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT
+    ## save some space by just keeping the needed binaries
+    find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete
+    find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete
+    if [[ "$created" == "yes" ]]; then
+        rm -rf $GIT_DIR
+    fi
 else
     cd $OPENMSGIT
-    git pull origin release/$VERSION.0-plus
+    git pull origin release/$VERSION.0
     cd -
 fi
 
@@ -65,7 +67,7 @@
 if conda env list | grep "$OPENMSENV"; then
     true
 else
-    conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
+    conda create -y --quiet --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 lxml
 # chmod -R u-w $OPENMSENV 
 fi
 ###############################################################################
@@ -101,33 +103,34 @@
 conda deactivate
 
 
-# ###############################################################################
-# ## copy all the test data files to test-data
-# ## most of it (outputs) will be overwritten later, but its needed for
-# ## prepare_test_data
-# ###############################################################################
+# # ###############################################################################
+# # ## copy all the test data files to test-data
+# # ## most of it (outputs) will be overwritten later, but its needed for
+# # ## prepare_test_data
+# # ###############################################################################
 echo "Get test data"
-find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete
+find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -delete
 
 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
 if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then 
-    wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
+    wget -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML
+    # wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
     mv MetaboliteSpectralDB.mzML test-data/
 fi
 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
 
-if [ ! -d test-data/pepnovo_models/ ]; then
-    mkdir -p /tmp/pepnovo
-    wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
-    unzip PepNovo.20120423.zip -d /tmp/pepnovo/
-    mv /tmp/pepnovo/Models test-data/pepnovo_models/
-    rm PepNovo.20120423.zip
-    rm -rf /tmp/pepnovo
-fi
+# if [ ! -d test-data/pepnovo_models/ ]; then
+#     mkdir -p /tmp/pepnovo
+#     wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+#     unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+#     mv /tmp/pepnovo/Models test-data/pepnovo_models/
+#     rm PepNovo.20120423.zip
+#     rm -rf /tmp/pepnovo
+# fi
 ###############################################################################
 ## generate ctd files using the binaries in the conda package 
 ###############################################################################
@@ -170,6 +173,47 @@
 ###############################################################################
 ## create script to create results for the tests and run it
 ###############################################################################
+# parse data preparation calls from OpenMS sources for a tool with a given id
+function prepare_test_data {
+#     id=$1
+# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
+
+    OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' |  sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g')
+    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
+    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
+        sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" |
+        grep -v "\.ini\.json" |
+        sed 's/.ini.json /ini /' | 
+        sed 's/#.*$//'| 
+        sed 's/^\s*//; s/\s*$//' | 
+        grep -v "^$"  | 
+        awk '{printf("%s@NEWLINE@", $0)}' | 
+        sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        sed 's/degenerate_cases\///' | 
+        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
+        grep add_test | 
+        egrep "TOPP|UTILS" |
+        sed 's@${DATA_DIR_SHARE}/@@g;'|
+        sed 's@${TMP_RIP_PATH}@./@g'|
+        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+    while read line
+    do
+        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
+
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+
+        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
+        # line="$(fix_tmp_files $line)"
+        echo 'echo executing "'$test_id'"'
+        echo "$line > $test_id.stdout 2> $test_id.stderr"
+        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
+    done
+}
+
 echo "Create test shell script"
 
 echo -n "" > prepare_test_data.sh
@@ -180,31 +224,19 @@
 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
 
 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
-echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
+echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh
 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
-echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
+echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh
 
 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
 
-## prepare_test_data > tmp_test_data.sh
-## # remove calls not needed for the tools listed in any .list file
-## echo LIST $LIST
-## if [ ! -z "$LIST" ]; then
-##     REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
-## else
-##     REX=".*"
-## fi
-## echo REX $REX
-## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
-## rm tmp_test_data.sh
-
 echo "Execute test shell script"
 chmod u+x prepare_test_data.sh
 cd ./test-data || exit
@@ -234,14 +266,11 @@
 for i in $(ls ctd/*ctd)
 do
     b=$(basename "$i" .ctd)
-    get_tests2 "$b" >> "$autotests"
+    ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests"
+    wc -l "$autotests"
 done
 echo "</macros>" >> "$autotests"
 
-# echo "Create test data links"
-# Breaks DecoyDatabase
-# link_tmp_files
-
 # tests for tools using output_prefix parameters can not be auto generated
 # hence we output the tests for manual curation in macros_test.xml
 # and remove them from the autotests
@@ -255,6 +284,7 @@
 #
 # not able to specify composite test data  
 # -> SpectraSTSearchAdapter 
+echo "Discard some tests"
 if [[ ! -z "$1" ]]; then
     echo "" > macros_discarded_auto.xml
     for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
@@ -272,7 +302,7 @@
 ## remove broken symlinks in test-data
 find test-data/ -xtype l -delete
 
-if [ ! -z "$created" ]; then
+if [[ "$created" == "yes" ]]; then
     echo "Removing temporary directory"
     rm -rf "$tmp"
 fi