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comparison SiriusAdapter.xml @ 10:b7505ec60b7d 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 21:30:01 +0000
parents 0c27444604dd
children
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9:0c27444604dd 10:b7505ec60b7d
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 2 <!--Proposed Tool Section: []-->
4 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description> 4 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SiriusAdapter</token> 6 <token name="@EXECUTABLE@">SiriusAdapter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 #if $sirius_executable:
18 mkdir sirius_executable &&
19 ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
20 #end if
21 mkdir in && 16 mkdir in &&
22 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
23 #if $in_featureinfo: 18 #if $in_featureinfo:
24 mkdir in_featureinfo && 19 mkdir in_featureinfo &&
25 ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' && 20 cp '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
26 #end if 21 #end if
27 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 22 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir out_sirius && 23 mkdir out_sirius &&
29 #end if 24 #end if
30 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 25 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir out_fingerid && 26 mkdir out_fingerid &&
32 #end if 27 #end if
33 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 28 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir out_ms && 29 mkdir out_ms &&
30 #end if
31 #if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 mkdir out_annotated_spectra &&
35 #end if 33 #end if
36 34
37 ## Main program call 35 ## Main program call
38 36
39 set -o pipefail && 37 set -o pipefail &&
40 @EXECUTABLE@ -write_ctd ./ && 38 @EXECUTABLE@ -write_ctd ./ &&
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43 #if $sirius_executable:
44 -sirius_executable
45 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
46 #end if
47 -in 41 -in
48 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
49 #if $in_featureinfo: 43 #if $in_featureinfo:
50 -in_featureinfo 44 -in_featureinfo
51 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' 45 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)'
60 #end if 54 #end if
61 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 55 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
62 -out_ms 56 -out_ms
63 'out_ms/output.${gxy2omsext("sirius.ms")}' 57 'out_ms/output.${gxy2omsext("sirius.ms")}'
64 #end if 58 #end if
59 #if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
60 -out_annotated_spectra
61 'out_annotated_spectra/output.${gxy2omsext("mzml")}'
62 #end if
65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 63 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
66 | tee '$stdout' 64 | tee '$stdout'
67 #end if 65 #end if
68 66
69 ## Postprocessing 67 ## Postprocessing
73 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 71 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 && mv 'out_fingerid/output.${gxy2omsext("mztab")}' '$out_fingerid' 72 && mv 'out_fingerid/output.${gxy2omsext("mztab")}' '$out_fingerid'
75 #end if 73 #end if
76 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 74 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
77 && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms' 75 && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms'
76 #end if
77 #if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
78 && mv 'out_annotated_spectra/output.${gxy2omsext("mzml")}' '$out_annotated_spectra'
78 #end if 79 #end if
79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 80 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
80 && mv '@EXECUTABLE@.ctd' '$ctd_out' 81 && mv '@EXECUTABLE@.ctd' '$ctd_out'
81 #end if]]></command> 82 #end if]]></command>
82 <configfiles> 83 <configfiles>
83 <inputs name="args_json" data_style="paths"/> 84 <inputs name="args_json" data_style="paths"/>
84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 85 <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
85 </configfiles> 86 </configfiles>
86 <inputs> 87 <inputs>
87 <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)"/> 88 <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
88 <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
89 <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/> 89 <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
90 <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help=""> 90 <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
91 <expand macro="list_string_san" name="out_project_space"/> 91 <expand macro="list_string_san" name="out_project_space"/>
92 </param> 92 </param>
93 <param argument="-sirius_user_email" type="text" optional="true" value="" label="E-mail for your SIRIUS account" help="">
94 <expand macro="list_string_san" name="sirius_user_email"/>
95 </param>
96 <param argument="-sirius_user_password" type="text" optional="true" value="" label="Password for your SIRIUS account" help="">
97 <expand macro="list_string_san" name="sirius_user_password"/>
98 </param>
93 <section name="preprocessing" title="" help="" expanded="false"> 99 <section name="preprocessing" title="" help="" expanded="false">
94 <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"/> 100 <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"/>
95 <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=""/> 101 <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=""/>
96 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help=""> 102 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
97 <option value="Da">Da</option> 103 <option value="Da">Da</option>
98 <option value="ppm" selected="true">ppm</option> 104 <option value="ppm" selected="true">ppm</option>
99 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/> 105 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
100 </param> 106 </param>
101 <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=""/> 107 <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=""/>
102 <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"/> 108 <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"/>
103 <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=""/> 109 <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=""/>
104 <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=""/> 110 <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=""/>
105 </section> 111 </section>
106 <section name="project" title="" help="" expanded="false"> 112 <section name="project" title="" help="" expanded="false">
107 <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"/> 113 <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"/>
114 <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">
115 <expand macro="list_string_san" name="loglevel"/>
116 </param>
108 <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=""/> 117 <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=""/>
109 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/> 118 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
110 </section> 119 </section>
111 <section name="sirius" title="" help="" expanded="false"> 120 <section name="sirius" title="" help="" expanded="false">
112 <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=""/> 121 <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=""/>
113 <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=""/> 122 <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=""/>
114 <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"/> 123 <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"/>
115 <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"/> 124 <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"/>
116 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/> 125 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
117 <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help=""> 126 <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
118 <option value="default">default</option> 127 <option value="default" selected="true">default</option>
119 <option value="qtof" selected="true">qtof</option> 128 <option value="qtof">qtof</option>
120 <option value="orbitrap">orbitrap</option> 129 <option value="orbitrap">orbitrap</option>
121 <option value="fticr">fticr</option> 130 <option value="fticr">fticr</option>
122 <expand macro="list_string_san" name="profile"/> 131 <expand macro="list_string_san" name="profile"/>
123 </param> 132 </param>
124 <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"> 133 <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">
125 <expand macro="list_string_san" name="formula"/> 134 <expand macro="list_string_san" name="formulas"/>
126 </param> 135 </param>
127 <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"> 136 <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">
128 <expand macro="list_string_san" name="ions_enforced"/> 137 <expand macro="list_string_san" name="ions_enforced"/>
129 </param> 138 </param>
130 <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=""/> 139 <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
131 <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"/> 140 <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"/>
132 <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"> 141 <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">
133 <expand macro="list_string_san" name="elements_considered"/> 142 <expand macro="list_string_san" name="elements_considered"/>
134 </param> 143 </param>
135 <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"> 144 <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">
136 <expand macro="list_string_san" name="elements_enforced"/> 145 <expand macro="list_string_san" name="elements_enforced"/>
137 </param> 146 </param>
138 <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/> 147 <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
139 <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"/> 148 <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"/>
140 <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"> 149 <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">
141 <expand macro="list_string_san" name="ions_considered"/> 150 <expand macro="list_string_san" name="ions_considered"/>
142 </param> 151 </param>
143 <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"> 152 <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">
144 <expand macro="list_string_san" name="db"/> 153 <expand macro="list_string_san" name="db"/>
145 </param> 154 </param>
155 <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/)">
156 <expand macro="list_string_san" name="solver"/>
157 </param>
146 </section> 158 </section>
147 <section name="fingerid" title="" help="" expanded="false"> 159 <section name="fingerid" title="" help="" expanded="false">
148 <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/> 160 <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">
149 <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">
150 <expand macro="list_string_san" name="db"/> 161 <expand macro="list_string_san" name="db"/>
151 </param> 162 </param>
152 </section> 163 </section>
153 <expand macro="adv_opts_macro"> 164 <expand macro="adv_opts_macro">
154 <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"/> 165 <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"/>
166 <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=""/>
155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 167 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 168 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
157 <expand macro="list_string_san" name="test"/> 169 <expand macro="list_string_san" name="test"/>
158 </param> 170 </param>
159 </expand> 171 </expand>
160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 172 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
161 <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option> 173 <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
162 <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> 174 <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>
163 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option> 175 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
176 <option value="out_annotated_spectra_FLAG">out_annotated_spectra (Export spectra with fragment annotations from SIRIUS)</option>
164 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 177 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
165 </param> 178 </param>
166 </inputs> 179 </inputs>
167 <outputs> 180 <outputs>
168 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab"> 181 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab">
172 <filter>OPTIONAL_OUTPUTS is not None and "out_fingerid_FLAG" in OPTIONAL_OUTPUTS</filter> 185 <filter>OPTIONAL_OUTPUTS is not None and "out_fingerid_FLAG" in OPTIONAL_OUTPUTS</filter>
173 </data> 186 </data>
174 <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms"> 187 <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms">
175 <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter> 188 <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter>
176 </data> 189 </data>
190 <data name="out_annotated_spectra" label="${tool.name} on ${on_string}: out_annotated_spectra" format="mzml">
191 <filter>OPTIONAL_OUTPUTS is not None and "out_annotated_spectra_FLAG" in OPTIONAL_OUTPUTS</filter>
192 </data>
177 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> 193 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
178 <filter>OPTIONAL_OUTPUTS is None</filter> 194 <filter>OPTIONAL_OUTPUTS is None</filter>
179 </data> 195 </data>
180 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 196 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
181 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 197 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
182 </data> 198 </data>
183 </outputs> 199 </outputs>
184 <tests><!-- TOPP_SiriusAdapter_1 --> 200 <tests/>
185 <test expect_num_outputs="2">
186 <section name="adv_opts">
187 <param name="converter_mode" value="false"/>
188 <param name="force" value="false"/>
189 <param name="test" value="true"/>
190 </section>
191 <param name="in" value="SiriusAdapter_1_input.mzML"/>
192 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
193 <param name="out_project_space" value=""/>
194 <section name="preprocessing">
195 <param name="filter_by_num_masstraces" value="1"/>
196 <param name="precursor_mz_tolerance" value="10.0"/>
197 <param name="precursor_mz_tolerance_unit" value="ppm"/>
198 <param name="precursor_rt_tolerance" value="5.0"/>
199 <param name="isotope_pattern_iterations" value="3"/>
200 <param name="feature_only" value="false"/>
201 <param name="no_masstrace_info_isotope_pattern" value="false"/>
202 </section>
203 <section name="project">
204 <param name="processors" value="1"/>
205 <param name="ignore_formula" value="false"/>
206 <param name="q" value="false"/>
207 </section>
208 <section name="sirius">
209 <param name="ppm_max" value="10.0"/>
210 <param name="ppm_max_ms2" value="10.0"/>
211 <param name="tree_timeout" value="0"/>
212 <param name="compound_timeout" value="100"/>
213 <param name="no_recalibration" value="false"/>
214 <param name="profile" value="qtof"/>
215 <param name="formula" value=""/>
216 <param name="ions_enforced" value=""/>
217 <param name="candidates" value="5"/>
218 <param name="candidates_per_ion" value="-1"/>
219 <param name="elements_considered" value=""/>
220 <param name="elements_enforced" value=""/>
221 <param name="no_isotope_score" value="false"/>
222 <param name="no_isotope_filter" value="false"/>
223 <param name="ions_considered" value=""/>
224 <param name="db" value="all"/>
225 </section>
226 <section name="fingerid">
227 <param name="candidates" value="10"/>
228 <param name="db" value="BIO"/>
229 </section>
230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
231 <output name="ctd_out" ftype="xml">
232 <assert_contents>
233 <is_valid_xml/>
234 </assert_contents>
235 </output>
236 </test>
237 <!-- TOPP_SiriusAdapter_2 -->
238 <test expect_num_outputs="2">
239 <section name="adv_opts">
240 <param name="converter_mode" value="false"/>
241 <param name="force" value="false"/>
242 <param name="test" value="true"/>
243 </section>
244 <param name="in" value="SiriusAdapter_2_input.mzML"/>
245 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
246 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
247 <param name="out_project_space" value=""/>
248 <section name="preprocessing">
249 <param name="filter_by_num_masstraces" value="3"/>
250 <param name="precursor_mz_tolerance" value="10.0"/>
251 <param name="precursor_mz_tolerance_unit" value="ppm"/>
252 <param name="precursor_rt_tolerance" value="5.0"/>
253 <param name="isotope_pattern_iterations" value="3"/>
254 <param name="feature_only" value="true"/>
255 <param name="no_masstrace_info_isotope_pattern" value="false"/>
256 </section>
257 <section name="project">
258 <param name="processors" value="1"/>
259 <param name="ignore_formula" value="false"/>
260 <param name="q" value="false"/>
261 </section>
262 <section name="sirius">
263 <param name="ppm_max" value="10.0"/>
264 <param name="ppm_max_ms2" value="10.0"/>
265 <param name="tree_timeout" value="0"/>
266 <param name="compound_timeout" value="100"/>
267 <param name="no_recalibration" value="false"/>
268 <param name="profile" value="qtof"/>
269 <param name="formula" value=""/>
270 <param name="ions_enforced" value=""/>
271 <param name="candidates" value="5"/>
272 <param name="candidates_per_ion" value="-1"/>
273 <param name="elements_considered" value=""/>
274 <param name="elements_enforced" value=""/>
275 <param name="no_isotope_score" value="false"/>
276 <param name="no_isotope_filter" value="false"/>
277 <param name="ions_considered" value=""/>
278 <param name="db" value="all"/>
279 </section>
280 <section name="fingerid">
281 <param name="candidates" value="10"/>
282 <param name="db" value="BIO"/>
283 </section>
284 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
285 <output name="ctd_out" ftype="xml">
286 <assert_contents>
287 <is_valid_xml/>
288 </assert_contents>
289 </output>
290 </test>
291 <!-- TOPP_SiriusAdapter_3 -->
292 <test expect_num_outputs="2">
293 <section name="adv_opts">
294 <param name="converter_mode" value="false"/>
295 <param name="force" value="false"/>
296 <param name="test" value="true"/>
297 </section>
298 <param name="in" value="SiriusAdapter_3_input.mzML"/>
299 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
300 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
301 <param name="out_project_space" value=""/>
302 <section name="preprocessing">
303 <param name="filter_by_num_masstraces" value="3"/>
304 <param name="precursor_mz_tolerance" value="10.0"/>
305 <param name="precursor_mz_tolerance_unit" value="ppm"/>
306 <param name="precursor_rt_tolerance" value="5.0"/>
307 <param name="isotope_pattern_iterations" value="3"/>
308 <param name="feature_only" value="false"/>
309 <param name="no_masstrace_info_isotope_pattern" value="false"/>
310 </section>
311 <section name="project">
312 <param name="processors" value="1"/>
313 <param name="ignore_formula" value="false"/>
314 <param name="q" value="false"/>
315 </section>
316 <section name="sirius">
317 <param name="ppm_max" value="10.0"/>
318 <param name="ppm_max_ms2" value="10.0"/>
319 <param name="tree_timeout" value="0"/>
320 <param name="compound_timeout" value="100"/>
321 <param name="no_recalibration" value="false"/>
322 <param name="profile" value="qtof"/>
323 <param name="formula" value=""/>
324 <param name="ions_enforced" value=""/>
325 <param name="candidates" value="5"/>
326 <param name="candidates_per_ion" value="-1"/>
327 <param name="elements_considered" value=""/>
328 <param name="elements_enforced" value=""/>
329 <param name="no_isotope_score" value="false"/>
330 <param name="no_isotope_filter" value="false"/>
331 <param name="ions_considered" value=""/>
332 <param name="db" value="all"/>
333 </section>
334 <section name="fingerid">
335 <param name="candidates" value="10"/>
336 <param name="db" value="BIO"/>
337 </section>
338 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
339 <output name="ctd_out" ftype="xml">
340 <assert_contents>
341 <is_valid_xml/>
342 </assert_contents>
343 </output>
344 </test>
345 <!-- TOPP_SiriusAdapter_5 -->
346 <test expect_num_outputs="2">
347 <section name="adv_opts">
348 <param name="converter_mode" value="true"/>
349 <param name="force" value="false"/>
350 <param name="test" value="true"/>
351 </section>
352 <param name="in" value="SiriusAdapter_3_input.mzML"/>
353 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
354 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
355 <param name="out_project_space" value=""/>
356 <section name="preprocessing">
357 <param name="filter_by_num_masstraces" value="1"/>
358 <param name="precursor_mz_tolerance" value="10.0"/>
359 <param name="precursor_mz_tolerance_unit" value="ppm"/>
360 <param name="precursor_rt_tolerance" value="5.0"/>
361 <param name="isotope_pattern_iterations" value="3"/>
362 <param name="feature_only" value="false"/>
363 <param name="no_masstrace_info_isotope_pattern" value="false"/>
364 </section>
365 <section name="project">
366 <param name="processors" value="1"/>
367 <param name="ignore_formula" value="false"/>
368 <param name="q" value="false"/>
369 </section>
370 <section name="sirius">
371 <param name="ppm_max" value="10.0"/>
372 <param name="ppm_max_ms2" value="10.0"/>
373 <param name="tree_timeout" value="0"/>
374 <param name="compound_timeout" value="100"/>
375 <param name="no_recalibration" value="false"/>
376 <param name="profile" value="qtof"/>
377 <param name="formula" value=""/>
378 <param name="ions_enforced" value=""/>
379 <param name="candidates" value="5"/>
380 <param name="candidates_per_ion" value="-1"/>
381 <param name="elements_considered" value=""/>
382 <param name="elements_enforced" value=""/>
383 <param name="no_isotope_score" value="false"/>
384 <param name="no_isotope_filter" value="false"/>
385 <param name="ions_considered" value=""/>
386 <param name="db" value=""/>
387 </section>
388 <section name="fingerid">
389 <param name="candidates" value="10"/>
390 <param name="db" value="BIO"/>
391 </section>
392 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
393 <output name="ctd_out" ftype="xml">
394 <assert_contents>
395 <is_valid_xml/>
396 </assert_contents>
397 </output>
398 </test>
399 <!-- TOPP_SiriusAdapter_6 -->
400 <test expect_num_outputs="2">
401 <section name="adv_opts">
402 <param name="converter_mode" value="true"/>
403 <param name="force" value="false"/>
404 <param name="test" value="true"/>
405 </section>
406 <param name="in" value="SiriusAdapter_4_input.mzML"/>
407 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
408 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
409 <param name="out_project_space" value=""/>
410 <section name="preprocessing">
411 <param name="filter_by_num_masstraces" value="1"/>
412 <param name="precursor_mz_tolerance" value="10.0"/>
413 <param name="precursor_mz_tolerance_unit" value="ppm"/>
414 <param name="precursor_rt_tolerance" value="5.0"/>
415 <param name="isotope_pattern_iterations" value="3"/>
416 <param name="feature_only" value="false"/>
417 <param name="no_masstrace_info_isotope_pattern" value="false"/>
418 </section>
419 <section name="project">
420 <param name="processors" value="1"/>
421 <param name="ignore_formula" value="false"/>
422 <param name="q" value="false"/>
423 </section>
424 <section name="sirius">
425 <param name="ppm_max" value="10.0"/>
426 <param name="ppm_max_ms2" value="10.0"/>
427 <param name="tree_timeout" value="0"/>
428 <param name="compound_timeout" value="100"/>
429 <param name="no_recalibration" value="false"/>
430 <param name="profile" value="qtof"/>
431 <param name="formula" value=""/>
432 <param name="ions_enforced" value=""/>
433 <param name="candidates" value="5"/>
434 <param name="candidates_per_ion" value="-1"/>
435 <param name="elements_considered" value=""/>
436 <param name="elements_enforced" value=""/>
437 <param name="no_isotope_score" value="false"/>
438 <param name="no_isotope_filter" value="false"/>
439 <param name="ions_considered" value=""/>
440 <param name="db" value=""/>
441 </section>
442 <section name="fingerid">
443 <param name="candidates" value="10"/>
444 <param name="db" value="BIO"/>
445 </section>
446 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
447 <output name="ctd_out" ftype="xml">
448 <assert_contents>
449 <is_valid_xml/>
450 </assert_contents>
451 </output>
452 </test>
453 <!-- TOPP_SiriusAdapter_8 -->
454 <test expect_num_outputs="2">
455 <section name="adv_opts">
456 <param name="converter_mode" value="false"/>
457 <param name="force" value="false"/>
458 <param name="test" value="true"/>
459 </section>
460 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
461 <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
462 <output name="out_sirius" file="SiriusAdapter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
463 <param name="out_project_space" value=""/>
464 <section name="preprocessing">
465 <param name="filter_by_num_masstraces" value="1"/>
466 <param name="precursor_mz_tolerance" value="10.0"/>
467 <param name="precursor_mz_tolerance_unit" value="ppm"/>
468 <param name="precursor_rt_tolerance" value="5.0"/>
469 <param name="isotope_pattern_iterations" value="3"/>
470 <param name="feature_only" value="true"/>
471 <param name="no_masstrace_info_isotope_pattern" value="false"/>
472 </section>
473 <section name="project">
474 <param name="processors" value="1"/>
475 <param name="ignore_formula" value="false"/>
476 <param name="q" value="false"/>
477 </section>
478 <section name="sirius">
479 <param name="ppm_max" value="10.0"/>
480 <param name="ppm_max_ms2" value="10.0"/>
481 <param name="tree_timeout" value="0"/>
482 <param name="compound_timeout" value="100"/>
483 <param name="no_recalibration" value="false"/>
484 <param name="profile" value="qtof"/>
485 <param name="formula" value=""/>
486 <param name="ions_enforced" value=""/>
487 <param name="candidates" value="5"/>
488 <param name="candidates_per_ion" value="-1"/>
489 <param name="elements_considered" value=""/>
490 <param name="elements_enforced" value=""/>
491 <param name="no_isotope_score" value="false"/>
492 <param name="no_isotope_filter" value="false"/>
493 <param name="ions_considered" value=""/>
494 <param name="db" value="all"/>
495 </section>
496 <section name="fingerid">
497 <param name="candidates" value="10"/>
498 <param name="db" value="BIO"/>
499 </section>
500 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
501 <output name="ctd_out" ftype="xml">
502 <assert_contents>
503 <is_valid_xml/>
504 </assert_contents>
505 </output>
506 </test>
507 <!-- TOPP_SiriusAdapter_9 -->
508 <test expect_num_outputs="2">
509 <section name="adv_opts">
510 <param name="converter_mode" value="false"/>
511 <param name="force" value="false"/>
512 <param name="test" value="true"/>
513 </section>
514 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
515 <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
516 <output name="out_sirius" file="SiriusAdapter_9_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
517 <param name="out_project_space" value=""/>
518 <section name="preprocessing">
519 <param name="filter_by_num_masstraces" value="1"/>
520 <param name="precursor_mz_tolerance" value="10.0"/>
521 <param name="precursor_mz_tolerance_unit" value="ppm"/>
522 <param name="precursor_rt_tolerance" value="5.0"/>
523 <param name="isotope_pattern_iterations" value="3"/>
524 <param name="feature_only" value="false"/>
525 <param name="no_masstrace_info_isotope_pattern" value="false"/>
526 </section>
527 <section name="project">
528 <param name="processors" value="1"/>
529 <param name="ignore_formula" value="false"/>
530 <param name="q" value="false"/>
531 </section>
532 <section name="sirius">
533 <param name="ppm_max" value="10.0"/>
534 <param name="ppm_max_ms2" value="10.0"/>
535 <param name="tree_timeout" value="0"/>
536 <param name="compound_timeout" value="100"/>
537 <param name="no_recalibration" value="false"/>
538 <param name="profile" value="qtof"/>
539 <param name="formula" value=""/>
540 <param name="ions_enforced" value=""/>
541 <param name="candidates" value="5"/>
542 <param name="candidates_per_ion" value="-1"/>
543 <param name="elements_considered" value=""/>
544 <param name="elements_enforced" value=""/>
545 <param name="no_isotope_score" value="false"/>
546 <param name="no_isotope_filter" value="false"/>
547 <param name="ions_considered" value=""/>
548 <param name="db" value="all"/>
549 </section>
550 <section name="fingerid">
551 <param name="candidates" value="10"/>
552 <param name="db" value="BIO"/>
553 </section>
554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
555 <output name="ctd_out" ftype="xml">
556 <assert_contents>
557 <is_valid_xml/>
558 </assert_contents>
559 </output>
560 </test>
561 <!-- TOPP_SiriusAdapter_7 -->
562 <test expect_num_outputs="2">
563 <section name="adv_opts">
564 <param name="converter_mode" value="false"/>
565 <param name="force" value="false"/>
566 <param name="test" value="true"/>
567 </section>
568 <param name="in" value="SiriusAdapter_4_input.mzML"/>
569 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
570 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
571 <param name="out_project_space" value=""/>
572 <section name="preprocessing">
573 <param name="filter_by_num_masstraces" value="1"/>
574 <param name="precursor_mz_tolerance" value="10.0"/>
575 <param name="precursor_mz_tolerance_unit" value="ppm"/>
576 <param name="precursor_rt_tolerance" value="5.0"/>
577 <param name="isotope_pattern_iterations" value="3"/>
578 <param name="feature_only" value="true"/>
579 <param name="no_masstrace_info_isotope_pattern" value="false"/>
580 </section>
581 <section name="project">
582 <param name="processors" value="1"/>
583 <param name="ignore_formula" value="false"/>
584 <param name="q" value="false"/>
585 </section>
586 <section name="sirius">
587 <param name="ppm_max" value="10.0"/>
588 <param name="ppm_max_ms2" value="10.0"/>
589 <param name="tree_timeout" value="0"/>
590 <param name="compound_timeout" value="100"/>
591 <param name="no_recalibration" value="false"/>
592 <param name="profile" value="qtof"/>
593 <param name="formula" value=""/>
594 <param name="ions_enforced" value=""/>
595 <param name="candidates" value="5"/>
596 <param name="candidates_per_ion" value="-1"/>
597 <param name="elements_considered" value=""/>
598 <param name="elements_enforced" value=""/>
599 <param name="no_isotope_score" value="false"/>
600 <param name="no_isotope_filter" value="false"/>
601 <param name="ions_considered" value=""/>
602 <param name="db" value="all"/>
603 </section>
604 <section name="fingerid">
605 <param name="candidates" value="10"/>
606 <param name="db" value="BIO"/>
607 </section>
608 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
609 <output name="ctd_out" ftype="xml">
610 <assert_contents>
611 <is_valid_xml/>
612 </assert_contents>
613 </output>
614 </test>
615 <!-- TOPP_SiriusAdapter_4 -->
616 <test expect_num_outputs="3">
617 <section name="adv_opts">
618 <param name="converter_mode" value="false"/>
619 <param name="force" value="false"/>
620 <param name="test" value="true"/>
621 </section>
622 <param name="in" value="SiriusAdapter_2_input.mzML"/>
623 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
624 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
625 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
626 <param name="out_project_space" value=""/>
627 <section name="preprocessing">
628 <param name="filter_by_num_masstraces" value="1"/>
629 <param name="precursor_mz_tolerance" value="10.0"/>
630 <param name="precursor_mz_tolerance_unit" value="ppm"/>
631 <param name="precursor_rt_tolerance" value="5.0"/>
632 <param name="isotope_pattern_iterations" value="3"/>
633 <param name="feature_only" value="false"/>
634 <param name="no_masstrace_info_isotope_pattern" value="false"/>
635 </section>
636 <section name="project">
637 <param name="processors" value="1"/>
638 <param name="ignore_formula" value="false"/>
639 <param name="q" value="false"/>
640 </section>
641 <section name="sirius">
642 <param name="ppm_max" value="10.0"/>
643 <param name="ppm_max_ms2" value="10.0"/>
644 <param name="tree_timeout" value="0"/>
645 <param name="compound_timeout" value="100"/>
646 <param name="no_recalibration" value="false"/>
647 <param name="profile" value="qtof"/>
648 <param name="formula" value=""/>
649 <param name="ions_enforced" value=""/>
650 <param name="candidates" value="5"/>
651 <param name="candidates_per_ion" value="-1"/>
652 <param name="elements_considered" value=""/>
653 <param name="elements_enforced" value=""/>
654 <param name="no_isotope_score" value="false"/>
655 <param name="no_isotope_filter" value="false"/>
656 <param name="ions_considered" value=""/>
657 <param name="db" value="ALL"/>
658 </section>
659 <section name="fingerid">
660 <param name="candidates" value="10"/>
661 <param name="db" value="BIO"/>
662 </section>
663 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
664 <output name="ctd_out" ftype="xml">
665 <assert_contents>
666 <is_valid_xml/>
667 </assert_contents>
668 </output>
669 </test>
670 </tests>
671 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry 201 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
672 202
673 203
674 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help> 204 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SiriusAdapter.html]]></help>
675 <expand macro="references"/> 205 <expand macro="references"/>
676 </tool> 206 </tool>