--- a/SiriusAdapter.xml	Thu Dec 01 19:16:56 2022 +0000
+++ b/SiriusAdapter.xml	Fri Jun 14 21:30:01 2024 +0000
@@ -1,6 +1,5 @@
-<?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: []-->
 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
   <macros>
@@ -14,15 +13,11 @@
 #import re
 
 ## Preprocessing
-#if $sirius_executable:
-  mkdir sirius_executable &&
-  ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
-#end if
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $in_featureinfo:
   mkdir in_featureinfo &&
-  ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
+  cp '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
 #end if
 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_sirius &&
@@ -33,6 +28,9 @@
 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_ms &&
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_annotated_spectra &&
+#end if
 
 ## Main program call
 
@@ -40,10 +38,6 @@
 @EXECUTABLE@ -write_ctd ./ &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
-#if $sirius_executable:
-  -sirius_executable
-  'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
-#end if
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 #if $in_featureinfo:
@@ -62,6 +56,10 @@
   -out_ms
   'out_ms/output.${gxy2omsext("sirius.ms")}'
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_annotated_spectra
+  'out_annotated_spectra/output.${gxy2omsext("mzml")}'
+#end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -76,84 +74,98 @@
 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms'
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_annotated_spectra/output.${gxy2omsext("mzml")}' '$out_annotated_spectra'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-sirius_executable" type="data" format="txt" optional="true" value="sirius" label="The Sirius executable" help="Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)"/>
-    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
     <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
     <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
       <expand macro="list_string_san" name="out_project_space"/>
     </param>
+    <param argument="-sirius_user_email" type="text" optional="true" value="" label="E-mail for your SIRIUS account" help="">
+      <expand macro="list_string_san" name="sirius_user_email"/>
+    </param>
+    <param argument="-sirius_user_password" type="text" optional="true" value="" label="Password for your SIRIUS account" help="">
+      <expand macro="list_string_san" name="sirius_user_password"/>
+    </param>
     <section name="preprocessing" title="" help="" expanded="false">
-      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
-      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help="">
+      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
+      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
       </param>
-      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
-      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
+      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
+      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
       <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
       <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
     </section>
     <section name="project" title="" help="" expanded="false">
-      <param name="processors" argument="-project:processors" type="integer" optional="true" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
+      <param name="maxmz" argument="-project:maxmz" type="integer" value="-1" label="Just consider compounds with a precursor mz lower or equal" help="this maximum mz. All other compounds in the input file. are ignored"/>
+      <param name="loglevel" argument="-project:loglevel" type="text" optional="true" value="" label="Set logging level of the Jobs SIRIUS will execute" help="Valid values: SEVERE, WARNING, INFO, FINER, ALL. Default: WARNING">
+        <expand macro="list_string_san" name="loglevel"/>
+      </param>
       <param name="ignore_formula" argument="-project:ignore_formula" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore given molecular formula in internal .ms format, while processing" help=""/>
       <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
     </section>
     <section name="sirius" title="" help="" expanded="false">
-      <param name="ppm_max" argument="-sirius:ppm_max" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
-      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
-      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
-      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
+      <param name="ppm_max" argument="-sirius:ppm_max" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
+      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
+      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
+      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
-      <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
-        <option value="default">default</option>
-        <option value="qtof" selected="true">qtof</option>
+      <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
+        <option value="default" selected="true">default</option>
+        <option value="qtof">qtof</option>
         <option value="orbitrap">orbitrap</option>
         <option value="fticr">fticr</option>
         <expand macro="list_string_san" name="profile"/>
       </param>
-      <param name="formula" argument="-sirius:formula" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
-        <expand macro="list_string_san" name="formula"/>
+      <param name="formulas" argument="-sirius:formulas" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
+        <expand macro="list_string_san" name="formulas"/>
       </param>
       <param name="ions_enforced" argument="-sirius:ions_enforced" type="text" optional="true" value="" label="The iontype/adduct of the MS/MS data" help="Example: [M+H]+, . [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a . comma separated list of adducts">
         <expand macro="list_string_san" name="ions_enforced"/>
       </param>
-      <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of formula candidates in the SIRIUS output" help=""/>
-      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" optional="true" value="-1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results. -1 omits parameter in Sirius"/>
-      <param name="elements_considered" argument="-sirius:elements_considered" type="text" optional="true" value="" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
+      <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
+      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" value="1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results"/>
+      <param name="elements_considered" argument="-sirius:elements_considered" type="text" value="SBrClBSe" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
         <expand macro="list_string_san" name="elements_considered"/>
       </param>
-      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" optional="true" value="" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound. Default is CHNOP">
+      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" value="CHNOP" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound">
         <expand macro="list_string_san" name="elements_enforced"/>
       </param>
       <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
       <param name="no_isotope_filter" argument="-sirius:no_isotope_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable molecular formula filte" help="When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score"/>
-      <param name="ions_considered" argument="-sirius:ions_considered" type="text" optional="true" value="" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
+      <param name="ions_considered" argument="-sirius:ions_considered" type="text" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
         <expand macro="list_string_san" name="ions_considered"/>
       </param>
-      <param name="db" argument="-sirius:db" type="text" optional="true" value="" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-sirius:db" type="text" value="none" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
+      <param name="solver" argument="-sirius:solver" type="text" value="CLP" label="For GUROBI and CPLEX environment variables need to be configured" help="(see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/)">
+        <expand macro="list_string_san" name="solver"/>
+      </param>
     </section>
     <section name="fingerid" title="" help="" expanded="false">
-      <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/>
-      <param name="db" argument="-fingerid:db" type="text" optional="true" value="BIO" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-fingerid:db" type="text" optional="true" value="" label="Search structures in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file" help="Without further SIRIUS processing"/>
+      <param argument="-read_sirius_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Read and print the standard output and error of the Sirius executable, even if it succeeds" help=""/>
       <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>
@@ -161,6 +173,7 @@
       <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
       <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
       <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
+      <option value="out_annotated_spectra_FLAG">out_annotated_spectra (Export spectra with fragment annotations from SIRIUS)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -174,6 +187,9 @@
     <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms">
       <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="out_annotated_spectra" label="${tool.name} on ${on_string}: out_annotated_spectra" format="mzml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_annotated_spectra_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
       <filter>OPTIONAL_OUTPUTS is None</filter>
     </data>
@@ -181,496 +197,10 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SiriusAdapter_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_1_input.mzML"/>
-      <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_3 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_5 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_6 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_8 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_9 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_9_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_7 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_4 -->
-    <test expect_num_outputs="3">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="ALL"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SiriusAdapter.html]]></help>
   <expand macro="references"/>
 </tool>