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comparison SiriusAdapter.xml @ 9:0c27444604dd draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:16:56 +0000
parents 2d655933d65f
children
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8:2d655933d65f 9:0c27444604dd
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--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]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> 4 <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> 5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SiriusAdapter</token> 7 <token name="@EXECUTABLE@">SiriusAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
17 #if $sirius_executable:
18 mkdir sirius_executable &&
19 ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
20 #end if
19 mkdir in && 21 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 22 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if $in_featureinfo: 23 #if $in_featureinfo:
22 mkdir in_featureinfo && 24 mkdir in_featureinfo &&
23 ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' && 25 ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
36 38
37 set -o pipefail && 39 set -o pipefail &&
38 @EXECUTABLE@ -write_ctd ./ && 40 @EXECUTABLE@ -write_ctd ./ &&
39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43 #if $sirius_executable:
44 -sirius_executable
45 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
46 #end if
41 -in 47 -in
42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 48 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
43 #if $in_featureinfo: 49 #if $in_featureinfo:
44 -in_featureinfo 50 -in_featureinfo
45 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' 51 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)'
73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
74 && mv '@EXECUTABLE@.ctd' '$ctd_out' 80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
75 #end if]]></command> 81 #end if]]></command>
76 <configfiles> 82 <configfiles>
77 <inputs name="args_json" data_style="paths"/> 83 <inputs name="args_json" data_style="paths"/>
78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile> 84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
79 </configfiles> 85 </configfiles>
80 <inputs> 86 <inputs>
81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> 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)"/>
82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/> 88 <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
83 <section name="preprocessing" title="Preprocessing" help="" expanded="false"> 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)"/>
84 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/> 90 <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
85 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/> 91 <expand macro="list_string_san" name="out_project_space"/>
86 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help=""> 92 </param>
87 <option value="Da" selected="true">Da</option> 93 <section name="preprocessing" title="" help="" expanded="false">
88 <option value="ppm">ppm</option> 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"/>
89 <expand macro="list_string_san"/> 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=""/>
90 </param> 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="">
91 <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="integer" optional="true" value="5" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/> 97 <option value="Da">Da</option>
98 <option value="ppm" selected="true">ppm</option>
99 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
100 </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=""/>
92 <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"/> 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"/>
93 <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=""/> 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=""/>
94 <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=""/> 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=""/>
95 </section> 105 </section>
96 <section name="sirius" title="Parameters for SIRIUS and CSI:FingerID" help="" expanded="false"> 106 <section name="project" title="" help="" expanded="false">
97 <param name="profile" argument="-sirius:profile" display="radio" type="select" optional="false" label="Specify the used analysis profile" help=""> 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"/>
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=""/>
109 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
110 </section>
111 <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=""/>
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=""/>
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"/>
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"/>
116 <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="">
118 <option value="default">default</option>
98 <option value="qtof" selected="true">qtof</option> 119 <option value="qtof" selected="true">qtof</option>
99 <option value="orbitrap">orbitrap</option> 120 <option value="orbitrap">orbitrap</option>
100 <option value="fticr">fticr</option> 121 <option value="fticr">fticr</option>
101 <expand macro="list_string_san"/> 122 <expand macro="list_string_san" name="profile"/>
102 </param> 123 </param>
103 <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of candidates in the SIRIUS output" help=""/> 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">
104 <param name="database" argument="-sirius:database" type="select" optional="false" label="search formulas in given database" help=""> 125 <expand macro="list_string_san" name="formula"/>
105 <option value="all" selected="true">all</option> 126 </param>
106 <option value="chebi">chebi</option> 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">
107 <option value="custom">custom</option> 128 <expand macro="list_string_san" name="ions_enforced"/>
108 <option value="kegg">kegg</option> 129 </param>
109 <option value="bio">bio</option> 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=""/>
110 <option value="natural products">natural products</option> 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"/>
111 <option value="pubmed">pubmed</option> 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">
112 <option value="hmdb">hmdb</option> 133 <expand macro="list_string_san" name="elements_considered"/>
113 <option value="biocyc">biocyc</option> 134 </param>
114 <option value="hsdb">hsdb</option> 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">
115 <option value="knapsack">knapsack</option> 136 <expand macro="list_string_san" name="elements_enforced"/>
116 <option value="biological">biological</option> 137 </param>
117 <option value="zinc bio">zinc bio</option> 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=""/>
118 <option value="gnps">gnps</option> 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"/>
119 <option value="pubchem">pubchem</option> 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">
120 <option value="mesh">mesh</option> 141 <expand macro="list_string_san" name="ions_considered"/>
121 <option value="maconda">maconda</option> 142 </param>
122 <expand macro="list_string_san"/> 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">
123 </param> 144 <expand macro="list_string_san" name="db"/>
124 <param name="noise" argument="-sirius:noise" type="integer" optional="true" min="0" value="0" label="median intensity of noise peaks" help=""/> 145 </param>
125 <param name="ppm_max" argument="-sirius:ppm_max" type="integer" optional="true" value="10" label="allowed ppm for decomposing masses" help=""/> 146 </section>
126 <param name="isotope" argument="-sirius:isotope" display="radio" type="select" optional="false" label="how to handle isotope pattern data" help="Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern"> 147 <section name="fingerid" title="" help="" expanded="false">
127 <option value="score">score</option> 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=""/>
128 <option value="filter">filter</option> 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">
129 <option value="both" selected="true">both</option> 150 <expand macro="list_string_san" name="db"/>
130 <option value="omit">omit</option> 151 </param>
131 <expand macro="list_string_san"/>
132 </param>
133 <param name="elements" argument="-sirius:elements" type="text" optional="true" value="CHNOP[5]S[8]Cl[1]" label="The allowed elements" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1]">
134 <expand macro="list_string_san"/>
135 </param>
136 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
137 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
138 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
139 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
140 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
141 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
142 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
143 </section> 152 </section>
144 <expand macro="adv_opts_macro"> 153 <expand macro="adv_opts_macro">
145 <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/> 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"/>
146 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
147 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
148 <expand macro="list_string_san"/> 157 <expand macro="list_string_san" name="test"/>
149 </param> 158 </param>
150 </expand> 159 </expand>
151 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
152 <option value="out_sirius_FLAG">out_sirius (MzTab Output file for SiriusAdapter results)</option> 161 <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
153 <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> 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>
154 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option> 163 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
155 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 164 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
156 </param> 165 </param>
157 </inputs> 166 </inputs>
170 </data> 179 </data>
171 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 180 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
172 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 181 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
173 </data> 182 </data>
174 </outputs> 183 </outputs>
175 <tests> 184 <tests><!-- TOPP_SiriusAdapter_1 -->
176 <expand macro="autotest_SiriusAdapter"/> 185 <test expect_num_outputs="2">
177 <expand macro="manutest_SiriusAdapter"/> 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>
178 </tests> 670 </tests>
179 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry 671 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
180 672
181 673
182 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SiriusAdapter.html]]></help> 674 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help>
183 <expand macro="references"/> 675 <expand macro="references"/>
184 </tool> 676 </tool>