Mercurial > repos > galaxyp > openms_assaygeneratormetabo

comparison AssayGeneratorMetabo.xml @ 6:f3ec820189ca draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:29:08 +0000
parents 83f5e5c1209c
children
comparison
equal deleted inserted replaced
5:83f5e5c1209c 6:f3ec820189ca
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: [Targeted Experiments and OpenSWATH]-->
4 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Assay library generation from DDA data (Metabolomics)</description> 4 <description>Assay library generation from DDA data (Metabolomics)</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">AssayGeneratorMetabo</token> 6 <token name="@EXECUTABLE@">AssayGeneratorMetabo</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_cond.in && 16 mkdir in_cond.in &&
22 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
23 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
24 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
25 #else 20 #else
26 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
27 #end if 22 #end if
28 mkdir in_id_cond.in_id && 23 mkdir in_id_cond.in_id &&
29 #if $in_id_cond.in_id_select == "no" 24 #if $in_id_cond.in_id_select == "no"
30 mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} && 25 mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} &&
31 ${' '.join(["ln -s '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])} 26 ${' '.join(["cp '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
32 #else 27 #else
33 ln -s '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' && 28 cp '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' &&
34 #end if 29 #end if
35 mkdir out && 30 mkdir out &&
36 31
37 ## Main program call 32 ## Main program call
38 33
39 set -o pipefail && 34 set -o pipefail &&
40 @EXECUTABLE@ -write_ctd ./ && 35 @EXECUTABLE@ -write_ctd ./ &&
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 37 @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 38 -in
48 #if $in_cond.in_select == "no" 39 #if $in_cond.in_select == "no"
49 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 40 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
50 #else 41 #else
51 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' 42 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
64 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
65 && mv '@EXECUTABLE@.ctd' '$ctd_out' 56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
66 #end if]]></command> 57 #end if]]></command>
67 <configfiles> 58 <configfiles>
68 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
69 <configfile name="hardcoded_json"><![CDATA[{"out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
70 </configfiles> 61 </configfiles>
71 <inputs> 62 <inputs>
72 <param argument="-sirius_executable" type="data" format="txt" optional="true" 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)"/>
73 <conditional name="in_cond"> 63 <conditional name="in_cond">
74 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 64 <param name="in_select" type="select" label="Run tool in batch mode for -in">
75 <option value="no">No: process all datasets jointly</option> 65 <option value="no">No: process all datasets jointly</option>
76 <option value="yes">Yes: process each dataset in an independent job</option> 66 <option value="yes">Yes: process each dataset in an independent job</option>
77 </param> 67 </param>
78 <when value="no"> 68 <when value="no">
79 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/> 69 <param argument="-in" type="data" format="mzml" multiple="true" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
80 </when> 70 </when>
81 <when value="yes"> 71 <when value="yes">
82 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/> 72 <param argument="-in" type="data" format="mzml" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
83 </when> 73 </when>
84 </conditional> 74 </conditional>
85 <conditional name="in_id_cond"> 75 <conditional name="in_id_cond">
86 <param name="in_id_select" type="select" label="Run tool in batch mode for -in_id"> 76 <param name="in_id_select" type="select" label="Run tool in batch mode for -in_id">
87 <option value="no">No: process all datasets jointly</option> 77 <option value="no">No: process all datasets jointly</option>
88 <option value="yes">Yes: process each dataset in an independent job</option> 78 <option value="yes">Yes: process each dataset in an independent job</option>
89 </param> 79 </param>
90 <when value="no"> 80 <when value="no">
91 <param argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/> 81 <param argument="-in_id" type="data" format="featurexml" multiple="true" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
92 </when> 82 </when>
93 <when value="yes"> 83 <when value="yes">
94 <param argument="-in_id" type="data" format="featurexml" multiple="false" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/> 84 <param argument="-in_id" type="data" format="featurexml" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
95 </when> 85 </when>
96 </conditional> 86 </conditional>
97 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)"> 87 <param name="out_type" type="select" label="File type of output out (Assay library output file)">
98 <option value="tsv">tabular (tsv)</option> 88 <option value="tsv">tabular (tsv)</option>
99 <option value="traML">traml</option> 89 <option value="traML">traml</option>
100 <option value="pqp">pqp</option> 90 <option value="pqp">pqp</option>
101 </param> 91 </param>
102 <param argument="-fragment_annotation" type="select" optional="true" label="Fragment annotation method" help=""> 92 <param argument="-fragment_annotation" type="select" label="Fragment annotation method" help="">
103 <option value="none">none</option> 93 <option value="none">none</option>
104 <option value="sirius" selected="true">sirius</option> 94 <option value="sirius" selected="true">sirius</option>
105 <expand macro="list_string_san" name="fragment_annotation"/> 95 <expand macro="list_string_san" name="fragment_annotation"/>
106 </param> 96 </param>
107 <param argument="-ambiguity_resolution_mz_tolerance" type="float" optional="true" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/> 97 <param argument="-ambiguity_resolution_mz_tolerance" type="float" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/>
108 <param argument="-ambiguity_resolution_rt_tolerance" type="float" optional="true" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/> 98 <param argument="-ambiguity_resolution_rt_tolerance" type="float" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/>
109 <param argument="-total_occurrence_filter" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/> 99 <param argument="-total_occurrence_filter" type="float" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
110 <param argument="-fragment_annotation_score_threshold" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/> 100 <param argument="-fragment_annotation_score_threshold" type="float" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
111 <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/> 101 <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/>
112 <param argument="-decoy_generation_method" type="select" optional="true" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)"> 102 <param argument="-decoy_generation_method" type="select" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
113 <option value="original" selected="true">original</option> 103 <option value="original" selected="true">original</option>
114 <option value="resolve_overlap">resolve_overlap</option> 104 <option value="resolve_overlap">resolve_overlap</option>
115 <option value="add_shift">add_shift</option> 105 <option value="add_shift">add_shift</option>
116 <option value="both">both</option> 106 <option value="both">both</option>
117 <expand macro="list_string_san" name="decoy_generation_method"/> 107 <expand macro="list_string_san" name="decoy_generation_method"/>
118 </param> 108 </param>
119 <param argument="-method" type="select" optional="true" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help=""> 109 <param argument="-method" type="select" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
120 <option value="highest_intensity" selected="true">highest_intensity</option> 110 <option value="highest_intensity" selected="true">highest_intensity</option>
121 <option value="consensus_spectrum">consensus_spectrum</option> 111 <option value="consensus_spectrum">consensus_spectrum</option>
122 <expand macro="list_string_san" name="method"/> 112 <expand macro="list_string_san" name="method"/>
123 </param> 113 </param>
124 <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/> 114 <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/>
125 <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/> 115 <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/>
126 <param argument="-precursor_mz_distance" type="float" optional="true" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/> 116 <param argument="-precursor_mz_distance" type="float" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
127 <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/> 117 <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/>
128 <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/> 118 <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
129 <param argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/> 119 <param argument="-min_transitions" type="integer" value="3" label="Minimal number of transitions" help=""/>
130 <param argument="-max_transitions" type="integer" optional="true" value="6" label="Maximal number of transitions" help=""/> 120 <param argument="-max_transitions" type="integer" value="6" label="Maximal number of transitions" help=""/>
131 <param argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/> 121 <param argument="-cosine_similarity_threshold" type="float" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
132 <param argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/> 122 <param argument="-transition_threshold" type="float" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
133 <section name="deisotoping" title="deisotoping" help="" expanded="false"> 123 <section name="deisotoping" title="deisotoping" help="" expanded="false">
134 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/> 124 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
135 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/> 125 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
136 <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" optional="true" label="Unit of the fragment tolerance" help=""> 126 <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" label="Unit of the fragment tolerance" help="">
137 <option value="ppm" selected="true">ppm</option> 127 <option value="ppm" selected="true">ppm</option>
138 <option value="Da">Da</option> 128 <option value="Da">Da</option>
139 <expand macro="list_string_san" name="fragment_unit"/> 129 <expand macro="list_string_san" name="fragment_unit"/>
140 </param> 130 </param>
141 <param name="min_charge" argument="-deisotoping:min_charge" type="integer" optional="true" min="1" value="1" label="The minimum charge considered" help=""/> 131 <param name="min_charge" argument="-deisotoping:min_charge" type="integer" min="1" value="1" label="The minimum charge considered" help=""/>
142 <param name="max_charge" argument="-deisotoping:max_charge" type="integer" optional="true" min="1" value="1" label="The maximum charge considered" help=""/> 132 <param name="max_charge" argument="-deisotoping:max_charge" type="integer" min="1" value="1" label="The maximum charge considered" help=""/>
143 <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" optional="true" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/> 133 <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
144 <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" optional="true" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/> 134 <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
145 <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/> 135 <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/>
146 <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/> 136 <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/>
147 </section> 137 </section>
148 <section name="preprocessing" title="" help="" expanded="false"> 138 <section name="preprocessing" title="" help="" expanded="false">
149 <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"/> 139 <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"/>
150 <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=""/> 140 <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=""/>
151 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help=""> 141 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
152 <option value="Da">Da</option> 142 <option value="Da">Da</option>
153 <option value="ppm" selected="true">ppm</option> 143 <option value="ppm" selected="true">ppm</option>
154 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/> 144 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
155 </param> 145 </param>
156 <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=""/> 146 <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=""/>
157 <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"/> 147 <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"/>
158 <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=""/> 148 <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=""/>
159 <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=""/> 149 <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=""/>
160 </section> 150 </section>
161 <section name="project" title="" help="" expanded="false"> 151 <section name="project" title="" help="" expanded="false">
162 <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"/> 152 <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"/>
153 <param name="processors" argument="-project:processors" type="integer" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
154 <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">
155 <expand macro="list_string_san" name="loglevel"/>
156 </param>
163 <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=""/> 157 <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=""/>
164 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/> 158 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
165 </section> 159 </section>
166 <section name="sirius" title="" help="" expanded="false"> 160 <section name="sirius" title="" help="" expanded="false">
167 <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=""/> 161 <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=""/>
168 <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=""/> 162 <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=""/>
169 <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"/> 163 <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"/>
170 <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"/> 164 <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"/>
171 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/> 165 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
172 <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help=""> 166 <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
173 <option value="default">default</option> 167 <option value="default" selected="true">default</option>
174 <option value="qtof" selected="true">qtof</option> 168 <option value="qtof">qtof</option>
175 <option value="orbitrap">orbitrap</option> 169 <option value="orbitrap">orbitrap</option>
176 <option value="fticr">fticr</option> 170 <option value="fticr">fticr</option>
177 <expand macro="list_string_san" name="profile"/> 171 <expand macro="list_string_san" name="profile"/>
178 </param> 172 </param>
179 <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"> 173 <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">
180 <expand macro="list_string_san" name="formula"/> 174 <expand macro="list_string_san" name="formulas"/>
181 </param> 175 </param>
182 <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"> 176 <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">
183 <expand macro="list_string_san" name="ions_enforced"/> 177 <expand macro="list_string_san" name="ions_enforced"/>
184 </param> 178 </param>
185 <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=""/> 179 <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
186 <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"/> 180 <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"/>
187 <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"> 181 <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">
188 <expand macro="list_string_san" name="elements_considered"/> 182 <expand macro="list_string_san" name="elements_considered"/>
189 </param> 183 </param>
190 <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"> 184 <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">
191 <expand macro="list_string_san" name="elements_enforced"/> 185 <expand macro="list_string_san" name="elements_enforced"/>
192 </param> 186 </param>
193 <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/> 187 <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
194 <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"/> 188 <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"/>
195 <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"> 189 <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">
196 <expand macro="list_string_san" name="ions_considered"/> 190 <expand macro="list_string_san" name="ions_considered"/>
197 </param> 191 </param>
198 <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"> 192 <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">
199 <expand macro="list_string_san" name="db"/> 193 <expand macro="list_string_san" name="db"/>
194 </param>
195 <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/)">
196 <expand macro="list_string_san" name="solver"/>
200 </param> 197 </param>
201 </section> 198 </section>
202 <section name="fingerid" title="" help="" expanded="false"> 199 <section name="fingerid" title="" help="" expanded="false">
203 <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/> 200 <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">
204 <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">
205 <expand macro="list_string_san" name="db"/> 201 <expand macro="list_string_san" name="db"/>
206 </param> 202 </param>
207 </section> 203 </section>
208 <expand macro="adv_opts_macro"> 204 <expand macro="adv_opts_macro">
209 <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="true" label="Unit of the ambiguity_resolution_mz_tolerance" help=""> 205 <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
210 <option value="ppm" selected="true">ppm</option> 206 <option value="ppm" selected="true">ppm</option>
211 <option value="Da">Da</option> 207 <option value="Da">Da</option>
212 <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/> 208 <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
213 </param> 209 </param>
214 <param argument="-precursor_recalibration_window" type="float" optional="true" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/> 210 <param argument="-precursor_recalibration_window" type="float" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
215 <param argument="-precursor_recalibration_window_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance_annotation" help=""> 211 <param argument="-precursor_recalibration_window_unit" type="select" label="Unit of the precursor_mz_tolerance_annotation" help="">
216 <option value="Da" selected="true">Da</option> 212 <option value="Da" selected="true">Da</option>
217 <option value="ppm">ppm</option> 213 <option value="ppm">ppm</option>
218 <expand macro="list_string_san" name="precursor_recalibration_window_unit"/> 214 <expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
219 </param> 215 </param>
220 <param argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/> 216 <param argument="-min_fragment_mz" type="float" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
221 <param argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/> 217 <param argument="-max_fragment_mz" type="float" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
218 <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=""/>
222 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 219 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
223 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 220 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
224 <expand macro="list_string_san" name="test"/> 221 <expand macro="list_string_san" name="test"/>
225 </param> 222 </param>
226 </expand> 223 </expand>
227 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 224 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
228 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 225 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
237 </data> 234 </data>
238 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 235 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
239 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 236 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
240 </data> 237 </data>
241 </outputs> 238 </outputs>
242 <tests><!-- UTILS_AssayGeneratorMetabo_1 --> 239 <tests>
240 <!-- TOPP_AssayGeneratorMetabo_1 -->
243 <test expect_num_outputs="2"> 241 <test expect_num_outputs="2">
244 <section name="adv_opts"> 242 <section name="adv_opts">
245 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> 243 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
246 <param name="precursor_recalibration_window" value="0.01"/> 244 <param name="precursor_recalibration_window" value="0.01"/>
247 <param name="precursor_recalibration_window_unit" value="Da"/> 245 <param name="precursor_recalibration_window_unit" value="Da"/>
248 <param name="min_fragment_mz" value="0.0"/> 246 <param name="min_fragment_mz" value="0.0"/>
249 <param name="max_fragment_mz" value="2000.0"/> 247 <param name="max_fragment_mz" value="2000.0"/>
248 <param name="read_sirius_stdout" value="false"/>
250 <param name="force" value="false"/> 249 <param name="force" value="false"/>
251 <param name="test" value="true"/> 250 <param name="test" value="true"/>
252 </section> 251 </section>
253 <conditional name="in_cond"> 252 <conditional name="in_cond">
254 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> 253 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
255 </conditional> 254 </conditional>
256 <conditional name="in_id_cond"> 255 <conditional name="in_id_cond">
257 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> 256 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
258 </conditional> 257 </conditional>
259 <param name="out_type" value="tsv"/> 258 <param name="out_type" value="tsv"/>
260 <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 259 <output name="out" value="AssayGeneratorMetabo_ffm_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
261 <param name="fragment_annotation" value="none"/> 260 <param name="fragment_annotation" value="none"/>
262 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> 261 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
263 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> 262 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
264 <param name="total_occurrence_filter" value="0.1"/> 263 <param name="total_occurrence_filter" value="0.1"/>
265 <param name="fragment_annotation_score_threshold" value="0.8"/> 264 <param name="fragment_annotation_score_threshold" value="0.8"/>
294 <param name="isotope_pattern_iterations" value="3"/> 293 <param name="isotope_pattern_iterations" value="3"/>
295 <param name="feature_only" value="false"/> 294 <param name="feature_only" value="false"/>
296 <param name="no_masstrace_info_isotope_pattern" value="false"/> 295 <param name="no_masstrace_info_isotope_pattern" value="false"/>
297 </section> 296 </section>
298 <section name="project"> 297 <section name="project">
298 <param name="maxmz" value="-1"/>
299 <param name="processors" value="1"/> 299 <param name="processors" value="1"/>
300 <param name="loglevel" value=""/>
300 <param name="ignore_formula" value="false"/> 301 <param name="ignore_formula" value="false"/>
301 <param name="q" value="false"/> 302 <param name="q" value="false"/>
302 </section> 303 </section>
303 <section name="sirius"> 304 <section name="sirius">
304 <param name="ppm_max" value="10.0"/> 305 <param name="ppm_max" value="10.0"/>
305 <param name="ppm_max_ms2" value="10.0"/> 306 <param name="ppm_max_ms2" value="10.0"/>
306 <param name="tree_timeout" value="0"/> 307 <param name="tree_timeout" value="100"/>
307 <param name="compound_timeout" value="100"/> 308 <param name="compound_timeout" value="100"/>
308 <param name="no_recalibration" value="false"/> 309 <param name="no_recalibration" value="false"/>
309 <param name="profile" value="qtof"/> 310 <param name="profile" value="default"/>
310 <param name="formula" value=""/> 311 <param name="formulas" value=""/>
311 <param name="ions_enforced" value=""/> 312 <param name="ions_enforced" value=""/>
312 <param name="candidates" value="5"/> 313 <param name="candidates" value="10"/>
313 <param name="candidates_per_ion" value="-1"/> 314 <param name="candidates_per_ion" value="1"/>
314 <param name="elements_considered" value=""/> 315 <param name="elements_considered" value="SBrClBSe"/>
315 <param name="elements_enforced" value=""/> 316 <param name="elements_enforced" value="CHNOP"/>
316 <param name="no_isotope_score" value="false"/> 317 <param name="no_isotope_score" value="false"/>
317 <param name="no_isotope_filter" value="false"/> 318 <param name="no_isotope_filter" value="false"/>
318 <param name="ions_considered" value=""/> 319 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
320 <param name="db" value="none"/>
321 <param name="solver" value="CLP"/>
322 </section>
323 <section name="fingerid">
319 <param name="db" value=""/> 324 <param name="db" value=""/>
320 </section>
321 <section name="fingerid">
322 <param name="candidates" value="10"/>
323 <param name="db" value="BIO"/>
324 </section> 325 </section>
325 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 326 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
326 <output name="ctd_out" ftype="xml"> 327 <output name="ctd_out" ftype="xml">
327 <assert_contents> 328 <assert_contents>
328 <is_valid_xml/> 329 <is_valid_xml/>
329 </assert_contents> 330 </assert_contents>
330 </output> 331 </output>
332 <assert_stdout>
333 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
334 </assert_stdout>
331 </test> 335 </test>
332 <!-- UTILS_AssayGeneratorMetabo_2 --> 336 <!-- TOPP_AssayGeneratorMetabo_2 -->
333 <test expect_num_outputs="2"> 337 <test expect_num_outputs="2">
334 <section name="adv_opts"> 338 <section name="adv_opts">
335 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> 339 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
336 <param name="precursor_recalibration_window" value="0.01"/> 340 <param name="precursor_recalibration_window" value="0.01"/>
337 <param name="precursor_recalibration_window_unit" value="Da"/> 341 <param name="precursor_recalibration_window_unit" value="Da"/>
338 <param name="min_fragment_mz" value="0.0"/> 342 <param name="min_fragment_mz" value="0.0"/>
339 <param name="max_fragment_mz" value="2000.0"/> 343 <param name="max_fragment_mz" value="2000.0"/>
344 <param name="read_sirius_stdout" value="false"/>
340 <param name="force" value="false"/> 345 <param name="force" value="false"/>
341 <param name="test" value="true"/> 346 <param name="test" value="true"/>
342 </section> 347 </section>
343 <conditional name="in_cond"> 348 <conditional name="in_cond">
344 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> 349 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
345 </conditional> 350 </conditional>
346 <conditional name="in_id_cond"> 351 <conditional name="in_id_cond">
347 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> 352 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
348 </conditional> 353 </conditional>
349 <param name="out_type" value="tsv"/> 354 <param name="out_type" value="tsv"/>
350 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 355 <output name="out" value="AssayGeneratorMetabo_ams_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
351 <param name="fragment_annotation" value="none"/> 356 <param name="fragment_annotation" value="none"/>
352 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> 357 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
353 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> 358 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
354 <param name="total_occurrence_filter" value="0.1"/> 359 <param name="total_occurrence_filter" value="0.1"/>
355 <param name="fragment_annotation_score_threshold" value="0.8"/> 360 <param name="fragment_annotation_score_threshold" value="0.8"/>
384 <param name="isotope_pattern_iterations" value="3"/> 389 <param name="isotope_pattern_iterations" value="3"/>
385 <param name="feature_only" value="false"/> 390 <param name="feature_only" value="false"/>
386 <param name="no_masstrace_info_isotope_pattern" value="false"/> 391 <param name="no_masstrace_info_isotope_pattern" value="false"/>
387 </section> 392 </section>
388 <section name="project"> 393 <section name="project">
394 <param name="maxmz" value="-1"/>
389 <param name="processors" value="1"/> 395 <param name="processors" value="1"/>
396 <param name="loglevel" value=""/>
390 <param name="ignore_formula" value="false"/> 397 <param name="ignore_formula" value="false"/>
391 <param name="q" value="false"/> 398 <param name="q" value="false"/>
392 </section> 399 </section>
393 <section name="sirius"> 400 <section name="sirius">
394 <param name="ppm_max" value="10.0"/> 401 <param name="ppm_max" value="10.0"/>
395 <param name="ppm_max_ms2" value="10.0"/> 402 <param name="ppm_max_ms2" value="10.0"/>
396 <param name="tree_timeout" value="0"/> 403 <param name="tree_timeout" value="100"/>
397 <param name="compound_timeout" value="100"/> 404 <param name="compound_timeout" value="100"/>
398 <param name="no_recalibration" value="false"/> 405 <param name="no_recalibration" value="false"/>
399 <param name="profile" value="qtof"/> 406 <param name="profile" value="default"/>
400 <param name="formula" value=""/> 407 <param name="formulas" value=""/>
401 <param name="ions_enforced" value=""/> 408 <param name="ions_enforced" value=""/>
402 <param name="candidates" value="5"/> 409 <param name="candidates" value="10"/>
403 <param name="candidates_per_ion" value="-1"/> 410 <param name="candidates_per_ion" value="1"/>
404 <param name="elements_considered" value=""/> 411 <param name="elements_considered" value="SBrClBSe"/>
405 <param name="elements_enforced" value=""/> 412 <param name="elements_enforced" value="CHNOP"/>
406 <param name="no_isotope_score" value="false"/> 413 <param name="no_isotope_score" value="false"/>
407 <param name="no_isotope_filter" value="false"/> 414 <param name="no_isotope_filter" value="false"/>
408 <param name="ions_considered" value=""/> 415 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
416 <param name="db" value="none"/>
417 <param name="solver" value="CLP"/>
418 </section>
419 <section name="fingerid">
409 <param name="db" value=""/> 420 <param name="db" value=""/>
410 </section>
411 <section name="fingerid">
412 <param name="candidates" value="10"/>
413 <param name="db" value="BIO"/>
414 </section> 421 </section>
415 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 422 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
416 <output name="ctd_out" ftype="xml"> 423 <output name="ctd_out" ftype="xml">
417 <assert_contents> 424 <assert_contents>
418 <is_valid_xml/> 425 <is_valid_xml/>
419 </assert_contents> 426 </assert_contents>
420 </output> 427 </output>
428 <assert_stdout>
429 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
430 </assert_stdout>
421 </test> 431 </test>
422 <!-- UTILS_AssayGeneratorMetabo_3 --> 432 <!-- TOPP_AssayGeneratorMetabo_3 -->
423 <test expect_num_outputs="2"> 433 <test expect_num_outputs="2">
424 <section name="adv_opts"> 434 <section name="adv_opts">
425 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> 435 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
426 <param name="precursor_recalibration_window" value="0.01"/> 436 <param name="precursor_recalibration_window" value="0.01"/>
427 <param name="precursor_recalibration_window_unit" value="Da"/> 437 <param name="precursor_recalibration_window_unit" value="Da"/>
428 <param name="min_fragment_mz" value="0.0"/> 438 <param name="min_fragment_mz" value="0.0"/>
429 <param name="max_fragment_mz" value="2000.0"/> 439 <param name="max_fragment_mz" value="2000.0"/>
440 <param name="read_sirius_stdout" value="false"/>
430 <param name="force" value="false"/> 441 <param name="force" value="false"/>
431 <param name="test" value="true"/> 442 <param name="test" value="true"/>
432 </section> 443 </section>
433 <conditional name="in_cond"> 444 <conditional name="in_cond">
434 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> 445 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
435 </conditional> 446 </conditional>
436 <conditional name="in_id_cond"> 447 <conditional name="in_id_cond">
437 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> 448 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
438 </conditional> 449 </conditional>
439 <param name="out_type" value="tsv"/> 450 <param name="out_type" value="tsv"/>
440 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 451 <output name="out" value="AssayGeneratorMetabo_ffm_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
441 <param name="fragment_annotation" value="none"/> 452 <param name="fragment_annotation" value="none"/>
442 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> 453 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
443 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> 454 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
444 <param name="total_occurrence_filter" value="0.1"/> 455 <param name="total_occurrence_filter" value="0.1"/>
445 <param name="fragment_annotation_score_threshold" value="0.8"/> 456 <param name="fragment_annotation_score_threshold" value="0.8"/>
474 <param name="isotope_pattern_iterations" value="3"/> 485 <param name="isotope_pattern_iterations" value="3"/>
475 <param name="feature_only" value="false"/> 486 <param name="feature_only" value="false"/>
476 <param name="no_masstrace_info_isotope_pattern" value="false"/> 487 <param name="no_masstrace_info_isotope_pattern" value="false"/>
477 </section> 488 </section>
478 <section name="project"> 489 <section name="project">
490 <param name="maxmz" value="-1"/>
479 <param name="processors" value="1"/> 491 <param name="processors" value="1"/>
492 <param name="loglevel" value=""/>
480 <param name="ignore_formula" value="false"/> 493 <param name="ignore_formula" value="false"/>
481 <param name="q" value="false"/> 494 <param name="q" value="false"/>
482 </section> 495 </section>
483 <section name="sirius"> 496 <section name="sirius">
484 <param name="ppm_max" value="10.0"/> 497 <param name="ppm_max" value="10.0"/>
485 <param name="ppm_max_ms2" value="10.0"/> 498 <param name="ppm_max_ms2" value="10.0"/>
486 <param name="tree_timeout" value="0"/> 499 <param name="tree_timeout" value="100"/>
487 <param name="compound_timeout" value="100"/> 500 <param name="compound_timeout" value="100"/>
488 <param name="no_recalibration" value="false"/> 501 <param name="no_recalibration" value="false"/>
489 <param name="profile" value="qtof"/> 502 <param name="profile" value="default"/>
490 <param name="formula" value=""/> 503 <param name="formulas" value=""/>
491 <param name="ions_enforced" value=""/> 504 <param name="ions_enforced" value=""/>
492 <param name="candidates" value="5"/> 505 <param name="candidates" value="10"/>
493 <param name="candidates_per_ion" value="-1"/> 506 <param name="candidates_per_ion" value="1"/>
494 <param name="elements_considered" value=""/> 507 <param name="elements_considered" value="SBrClBSe"/>
495 <param name="elements_enforced" value=""/> 508 <param name="elements_enforced" value="CHNOP"/>
496 <param name="no_isotope_score" value="false"/> 509 <param name="no_isotope_score" value="false"/>
497 <param name="no_isotope_filter" value="false"/> 510 <param name="no_isotope_filter" value="false"/>
498 <param name="ions_considered" value=""/> 511 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
512 <param name="db" value="none"/>
513 <param name="solver" value="CLP"/>
514 </section>
515 <section name="fingerid">
499 <param name="db" value=""/> 516 <param name="db" value=""/>
500 </section>
501 <section name="fingerid">
502 <param name="candidates" value="10"/>
503 <param name="db" value="BIO"/>
504 </section> 517 </section>
505 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
506 <output name="ctd_out" ftype="xml"> 519 <output name="ctd_out" ftype="xml">
507 <assert_contents> 520 <assert_contents>
508 <is_valid_xml/> 521 <is_valid_xml/>
509 </assert_contents> 522 </assert_contents>
510 </output> 523 </output>
524 <assert_stdout>
525 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
526 </assert_stdout>
511 </test> 527 </test>
512 <!-- UTILS_AssayGeneratorMetabo_4 --> 528 <!-- TOPP_AssayGeneratorMetabo_4 -->
513 <test expect_num_outputs="2"> 529 <test expect_num_outputs="2">
514 <section name="adv_opts"> 530 <section name="adv_opts">
515 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> 531 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
516 <param name="precursor_recalibration_window" value="0.01"/> 532 <param name="precursor_recalibration_window" value="0.01"/>
517 <param name="precursor_recalibration_window_unit" value="Da"/> 533 <param name="precursor_recalibration_window_unit" value="Da"/>
518 <param name="min_fragment_mz" value="0.0"/> 534 <param name="min_fragment_mz" value="0.0"/>
519 <param name="max_fragment_mz" value="2000.0"/> 535 <param name="max_fragment_mz" value="2000.0"/>
536 <param name="read_sirius_stdout" value="false"/>
520 <param name="force" value="false"/> 537 <param name="force" value="false"/>
521 <param name="test" value="true"/> 538 <param name="test" value="true"/>
522 </section> 539 </section>
523 <conditional name="in_cond"> 540 <conditional name="in_cond">
524 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> 541 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
525 </conditional> 542 </conditional>
526 <conditional name="in_id_cond"> 543 <conditional name="in_id_cond">
527 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> 544 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
528 </conditional> 545 </conditional>
529 <param name="out_type" value="tsv"/> 546 <param name="out_type" value="tsv"/>
530 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 547 <output name="out" value="AssayGeneratorMetabo_ams_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
531 <param name="fragment_annotation" value="none"/> 548 <param name="fragment_annotation" value="none"/>
532 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> 549 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
533 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> 550 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
534 <param name="total_occurrence_filter" value="0.1"/> 551 <param name="total_occurrence_filter" value="0.1"/>
535 <param name="fragment_annotation_score_threshold" value="0.8"/> 552 <param name="fragment_annotation_score_threshold" value="0.8"/>
564 <param name="isotope_pattern_iterations" value="3"/> 581 <param name="isotope_pattern_iterations" value="3"/>
565 <param name="feature_only" value="false"/> 582 <param name="feature_only" value="false"/>
566 <param name="no_masstrace_info_isotope_pattern" value="false"/> 583 <param name="no_masstrace_info_isotope_pattern" value="false"/>
567 </section> 584 </section>
568 <section name="project"> 585 <section name="project">
586 <param name="maxmz" value="-1"/>
569 <param name="processors" value="1"/> 587 <param name="processors" value="1"/>
588 <param name="loglevel" value=""/>
570 <param name="ignore_formula" value="false"/> 589 <param name="ignore_formula" value="false"/>
571 <param name="q" value="false"/> 590 <param name="q" value="false"/>
572 </section> 591 </section>
573 <section name="sirius"> 592 <section name="sirius">
574 <param name="ppm_max" value="10.0"/> 593 <param name="ppm_max" value="10.0"/>
575 <param name="ppm_max_ms2" value="10.0"/> 594 <param name="ppm_max_ms2" value="10.0"/>
576 <param name="tree_timeout" value="0"/> 595 <param name="tree_timeout" value="100"/>
577 <param name="compound_timeout" value="100"/> 596 <param name="compound_timeout" value="100"/>
578 <param name="no_recalibration" value="false"/> 597 <param name="no_recalibration" value="false"/>
579 <param name="profile" value="qtof"/> 598 <param name="profile" value="default"/>
580 <param name="formula" value=""/> 599 <param name="formulas" value=""/>
581 <param name="ions_enforced" value=""/> 600 <param name="ions_enforced" value=""/>
582 <param name="candidates" value="5"/> 601 <param name="candidates" value="10"/>
583 <param name="candidates_per_ion" value="-1"/> 602 <param name="candidates_per_ion" value="1"/>
584 <param name="elements_considered" value=""/> 603 <param name="elements_considered" value="SBrClBSe"/>
585 <param name="elements_enforced" value=""/> 604 <param name="elements_enforced" value="CHNOP"/>
586 <param name="no_isotope_score" value="false"/> 605 <param name="no_isotope_score" value="false"/>
587 <param name="no_isotope_filter" value="false"/> 606 <param name="no_isotope_filter" value="false"/>
588 <param name="ions_considered" value=""/> 607 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
608 <param name="db" value="none"/>
609 <param name="solver" value="CLP"/>
610 </section>
611 <section name="fingerid">
589 <param name="db" value=""/> 612 <param name="db" value=""/>
590 </section>
591 <section name="fingerid">
592 <param name="candidates" value="10"/>
593 <param name="db" value="BIO"/>
594 </section> 613 </section>
595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 614 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
596 <output name="ctd_out" ftype="xml"> 615 <output name="ctd_out" ftype="xml">
597 <assert_contents> 616 <assert_contents>
598 <is_valid_xml/> 617 <is_valid_xml/>
599 </assert_contents> 618 </assert_contents>
600 </output> 619 </output>
620 <assert_stdout>
621 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
622 </assert_stdout>
601 </test> 623 </test>
602 <!-- UTILS_AssayGeneratorMetabo_5 --> 624 <!-- TOPP_AssayGeneratorMetabo_5 -->
603 <test expect_num_outputs="2"> 625 <test expect_num_outputs="2">
604 <section name="adv_opts"> 626 <section name="adv_opts">
605 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> 627 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
606 <param name="precursor_recalibration_window" value="0.01"/> 628 <param name="precursor_recalibration_window" value="0.01"/>
607 <param name="precursor_recalibration_window_unit" value="Da"/> 629 <param name="precursor_recalibration_window_unit" value="Da"/>
608 <param name="min_fragment_mz" value="0.0"/> 630 <param name="min_fragment_mz" value="0.0"/>
609 <param name="max_fragment_mz" value="2000.0"/> 631 <param name="max_fragment_mz" value="2000.0"/>
632 <param name="read_sirius_stdout" value="false"/>
610 <param name="force" value="false"/> 633 <param name="force" value="false"/>
611 <param name="test" value="true"/> 634 <param name="test" value="true"/>
612 </section> 635 </section>
613 <conditional name="in_cond"> 636 <conditional name="in_cond">
614 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> 637 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
615 </conditional> 638 </conditional>
616 <conditional name="in_id_cond"> 639 <conditional name="in_id_cond">
617 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> 640 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
618 </conditional> 641 </conditional>
619 <param name="out_type" value="tsv"/> 642 <param name="out_type" value="tsv"/>
620 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 643 <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
621 <param name="fragment_annotation" value="none"/> 644 <param name="fragment_annotation" value="none"/>
622 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> 645 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
623 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> 646 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
624 <param name="total_occurrence_filter" value="0.1"/> 647 <param name="total_occurrence_filter" value="0.1"/>
625 <param name="fragment_annotation_score_threshold" value="0.8"/> 648 <param name="fragment_annotation_score_threshold" value="0.8"/>
654 <param name="isotope_pattern_iterations" value="3"/> 677 <param name="isotope_pattern_iterations" value="3"/>
655 <param name="feature_only" value="false"/> 678 <param name="feature_only" value="false"/>
656 <param name="no_masstrace_info_isotope_pattern" value="false"/> 679 <param name="no_masstrace_info_isotope_pattern" value="false"/>
657 </section> 680 </section>
658 <section name="project"> 681 <section name="project">
682 <param name="maxmz" value="-1"/>
659 <param name="processors" value="1"/> 683 <param name="processors" value="1"/>
684 <param name="loglevel" value=""/>
660 <param name="ignore_formula" value="false"/> 685 <param name="ignore_formula" value="false"/>
661 <param name="q" value="false"/> 686 <param name="q" value="false"/>
662 </section> 687 </section>
663 <section name="sirius"> 688 <section name="sirius">
664 <param name="ppm_max" value="10.0"/> 689 <param name="ppm_max" value="10.0"/>
665 <param name="ppm_max_ms2" value="10.0"/> 690 <param name="ppm_max_ms2" value="10.0"/>
666 <param name="tree_timeout" value="0"/> 691 <param name="tree_timeout" value="100"/>
667 <param name="compound_timeout" value="100"/> 692 <param name="compound_timeout" value="100"/>
668 <param name="no_recalibration" value="false"/> 693 <param name="no_recalibration" value="false"/>
669 <param name="profile" value="qtof"/> 694 <param name="profile" value="default"/>
670 <param name="formula" value=""/> 695 <param name="formulas" value=""/>
671 <param name="ions_enforced" value=""/> 696 <param name="ions_enforced" value=""/>
672 <param name="candidates" value="5"/> 697 <param name="candidates" value="10"/>
673 <param name="candidates_per_ion" value="-1"/> 698 <param name="candidates_per_ion" value="1"/>
674 <param name="elements_considered" value=""/> 699 <param name="elements_considered" value="SBrClBSe"/>
675 <param name="elements_enforced" value=""/> 700 <param name="elements_enforced" value="CHNOP"/>
676 <param name="no_isotope_score" value="false"/> 701 <param name="no_isotope_score" value="false"/>
677 <param name="no_isotope_filter" value="false"/> 702 <param name="no_isotope_filter" value="false"/>
678 <param name="ions_considered" value=""/> 703 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
704 <param name="db" value="none"/>
705 <param name="solver" value="CLP"/>
706 </section>
707 <section name="fingerid">
679 <param name="db" value=""/> 708 <param name="db" value=""/>
680 </section>
681 <section name="fingerid">
682 <param name="candidates" value="10"/>
683 <param name="db" value="BIO"/>
684 </section> 709 </section>
685 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 710 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
686 <output name="ctd_out" ftype="xml"> 711 <output name="ctd_out" ftype="xml">
687 <assert_contents> 712 <assert_contents>
688 <is_valid_xml/> 713 <is_valid_xml/>
689 </assert_contents> 714 </assert_contents>
690 </output> 715 </output>
691 </test> 716 <assert_stdout>
692 <!-- UTILS_AssayGeneratorMetabo_7 --> 717 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
693 <test expect_num_outputs="2"> 718 </assert_stdout>
694 <section name="adv_opts">
695 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
696 <param name="precursor_recalibration_window" value="0.01"/>
697 <param name="precursor_recalibration_window_unit" value="Da"/>
698 <param name="min_fragment_mz" value="0.0"/>
699 <param name="max_fragment_mz" value="2000.0"/>
700 <param name="force" value="false"/>
701 <param name="test" value="true"/>
702 </section>
703 <conditional name="in_cond">
704 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
705 </conditional>
706 <conditional name="in_id_cond">
707 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
708 </conditional>
709 <param name="out_type" value="tsv"/>
710 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
711 <param name="fragment_annotation" value="sirius"/>
712 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
713 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
714 <param name="total_occurrence_filter" value="0.1"/>
715 <param name="fragment_annotation_score_threshold" value="0.8"/>
716 <param name="decoy_generation" value="false"/>
717 <param name="decoy_generation_method" value="original"/>
718 <param name="method" value="highest_intensity"/>
719 <param name="use_exact_mass" value="true"/>
720 <param name="exclude_ms2_precursor" value="false"/>
721 <param name="precursor_mz_distance" value="0.0001"/>
722 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
723 <param name="use_known_unknowns" value="false"/>
724 <param name="min_transitions" value="2"/>
725 <param name="max_transitions" value="3"/>
726 <param name="cosine_similarity_threshold" value="0.98"/>
727 <param name="transition_threshold" value="3.0"/>
728 <section name="deisotoping">
729 <param name="use_deisotoper" value="false"/>
730 <param name="fragment_tolerance" value="1.0"/>
731 <param name="fragment_unit" value="ppm"/>
732 <param name="min_charge" value="1"/>
733 <param name="max_charge" value="1"/>
734 <param name="min_isopeaks" value="2"/>
735 <param name="max_isopeaks" value="3"/>
736 <param name="keep_only_deisotoped" value="false"/>
737 <param name="annotate_charge" value="false"/>
738 </section>
739 <section name="preprocessing">
740 <param name="filter_by_num_masstraces" value="1"/>
741 <param name="precursor_mz_tolerance" value="10.0"/>
742 <param name="precursor_mz_tolerance_unit" value="ppm"/>
743 <param name="precursor_rt_tolerance" value="5.0"/>
744 <param name="isotope_pattern_iterations" value="3"/>
745 <param name="feature_only" value="true"/>
746 <param name="no_masstrace_info_isotope_pattern" value="false"/>
747 </section>
748 <section name="project">
749 <param name="processors" value="1"/>
750 <param name="ignore_formula" value="false"/>
751 <param name="q" value="false"/>
752 </section>
753 <section name="sirius">
754 <param name="ppm_max" value="10.0"/>
755 <param name="ppm_max_ms2" value="10.0"/>
756 <param name="tree_timeout" value="0"/>
757 <param name="compound_timeout" value="100"/>
758 <param name="no_recalibration" value="false"/>
759 <param name="profile" value="qtof"/>
760 <param name="formula" value=""/>
761 <param name="ions_enforced" value=""/>
762 <param name="candidates" value="5"/>
763 <param name="candidates_per_ion" value="-1"/>
764 <param name="elements_considered" value=""/>
765 <param name="elements_enforced" value=""/>
766 <param name="no_isotope_score" value="false"/>
767 <param name="no_isotope_filter" value="false"/>
768 <param name="ions_considered" value=""/>
769 <param name="db" value=""/>
770 </section>
771 <section name="fingerid">
772 <param name="candidates" value="10"/>
773 <param name="db" value="BIO"/>
774 </section>
775 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
776 <output name="ctd_out" ftype="xml">
777 <assert_contents>
778 <is_valid_xml/>
779 </assert_contents>
780 </output>
781 </test>
782 <!-- UTILS_AssayGeneratorMetabo_8 -->
783 <test expect_num_outputs="2">
784 <section name="adv_opts">
785 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
786 <param name="precursor_recalibration_window" value="0.01"/>
787 <param name="precursor_recalibration_window_unit" value="Da"/>
788 <param name="min_fragment_mz" value="0.0"/>
789 <param name="max_fragment_mz" value="2000.0"/>
790 <param name="force" value="false"/>
791 <param name="test" value="true"/>
792 </section>
793 <conditional name="in_cond">
794 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
795 </conditional>
796 <conditional name="in_id_cond">
797 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
798 </conditional>
799 <param name="out_type" value="tsv"/>
800 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
801 <param name="fragment_annotation" value="sirius"/>
802 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
803 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
804 <param name="total_occurrence_filter" value="0.1"/>
805 <param name="fragment_annotation_score_threshold" value="0.8"/>
806 <param name="decoy_generation" value="false"/>
807 <param name="decoy_generation_method" value="original"/>
808 <param name="method" value="highest_intensity"/>
809 <param name="use_exact_mass" value="true"/>
810 <param name="exclude_ms2_precursor" value="false"/>
811 <param name="precursor_mz_distance" value="0.0001"/>
812 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
813 <param name="use_known_unknowns" value="true"/>
814 <param name="min_transitions" value="2"/>
815 <param name="max_transitions" value="3"/>
816 <param name="cosine_similarity_threshold" value="0.98"/>
817 <param name="transition_threshold" value="3.0"/>
818 <section name="deisotoping">
819 <param name="use_deisotoper" value="false"/>
820 <param name="fragment_tolerance" value="1.0"/>
821 <param name="fragment_unit" value="ppm"/>
822 <param name="min_charge" value="1"/>
823 <param name="max_charge" value="1"/>
824 <param name="min_isopeaks" value="2"/>
825 <param name="max_isopeaks" value="3"/>
826 <param name="keep_only_deisotoped" value="false"/>
827 <param name="annotate_charge" value="false"/>
828 </section>
829 <section name="preprocessing">
830 <param name="filter_by_num_masstraces" value="1"/>
831 <param name="precursor_mz_tolerance" value="10.0"/>
832 <param name="precursor_mz_tolerance_unit" value="ppm"/>
833 <param name="precursor_rt_tolerance" value="5.0"/>
834 <param name="isotope_pattern_iterations" value="3"/>
835 <param name="feature_only" value="true"/>
836 <param name="no_masstrace_info_isotope_pattern" value="false"/>
837 </section>
838 <section name="project">
839 <param name="processors" value="1"/>
840 <param name="ignore_formula" value="false"/>
841 <param name="q" value="false"/>
842 </section>
843 <section name="sirius">
844 <param name="ppm_max" value="10.0"/>
845 <param name="ppm_max_ms2" value="10.0"/>
846 <param name="tree_timeout" value="0"/>
847 <param name="compound_timeout" value="100"/>
848 <param name="no_recalibration" value="false"/>
849 <param name="profile" value="qtof"/>
850 <param name="formula" value=""/>
851 <param name="ions_enforced" value=""/>
852 <param name="candidates" value="5"/>
853 <param name="candidates_per_ion" value="-1"/>
854 <param name="elements_considered" value=""/>
855 <param name="elements_enforced" value=""/>
856 <param name="no_isotope_score" value="false"/>
857 <param name="no_isotope_filter" value="false"/>
858 <param name="ions_considered" value=""/>
859 <param name="db" value="ALL"/>
860 </section>
861 <section name="fingerid">
862 <param name="candidates" value="10"/>
863 <param name="db" value="BIO"/>
864 </section>
865 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
866 <output name="ctd_out" ftype="xml">
867 <assert_contents>
868 <is_valid_xml/>
869 </assert_contents>
870 </output>
871 </test>
872 <!-- UTILS_AssayGeneratorMetabo_9 -->
873 <test expect_num_outputs="2">
874 <section name="adv_opts">
875 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
876 <param name="precursor_recalibration_window" value="0.01"/>
877 <param name="precursor_recalibration_window_unit" value="Da"/>
878 <param name="min_fragment_mz" value="0.0"/>
879 <param name="max_fragment_mz" value="2000.0"/>
880 <param name="force" value="false"/>
881 <param name="test" value="true"/>
882 </section>
883 <conditional name="in_cond">
884 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
885 </conditional>
886 <conditional name="in_id_cond">
887 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
888 </conditional>
889 <param name="out_type" value="tsv"/>
890 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
891 <param name="fragment_annotation" value="sirius"/>
892 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
893 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
894 <param name="total_occurrence_filter" value="0.1"/>
895 <param name="fragment_annotation_score_threshold" value="0.8"/>
896 <param name="decoy_generation" value="false"/>
897 <param name="decoy_generation_method" value="original"/>
898 <param name="method" value="highest_intensity"/>
899 <param name="use_exact_mass" value="true"/>
900 <param name="exclude_ms2_precursor" value="false"/>
901 <param name="precursor_mz_distance" value="0.0001"/>
902 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
903 <param name="use_known_unknowns" value="false"/>
904 <param name="min_transitions" value="2"/>
905 <param name="max_transitions" value="3"/>
906 <param name="cosine_similarity_threshold" value="0.98"/>
907 <param name="transition_threshold" value="3.0"/>
908 <section name="deisotoping">
909 <param name="use_deisotoper" value="false"/>
910 <param name="fragment_tolerance" value="1.0"/>
911 <param name="fragment_unit" value="ppm"/>
912 <param name="min_charge" value="1"/>
913 <param name="max_charge" value="1"/>
914 <param name="min_isopeaks" value="2"/>
915 <param name="max_isopeaks" value="3"/>
916 <param name="keep_only_deisotoped" value="false"/>
917 <param name="annotate_charge" value="false"/>
918 </section>
919 <section name="preprocessing">
920 <param name="filter_by_num_masstraces" value="1"/>
921 <param name="precursor_mz_tolerance" value="10.0"/>
922 <param name="precursor_mz_tolerance_unit" value="ppm"/>
923 <param name="precursor_rt_tolerance" value="5.0"/>
924 <param name="isotope_pattern_iterations" value="3"/>
925 <param name="feature_only" value="true"/>
926 <param name="no_masstrace_info_isotope_pattern" value="false"/>
927 </section>
928 <section name="project">
929 <param name="processors" value="1"/>
930 <param name="ignore_formula" value="false"/>
931 <param name="q" value="false"/>
932 </section>
933 <section name="sirius">
934 <param name="ppm_max" value="10.0"/>
935 <param name="ppm_max_ms2" value="10.0"/>
936 <param name="tree_timeout" value="0"/>
937 <param name="compound_timeout" value="100"/>
938 <param name="no_recalibration" value="false"/>
939 <param name="profile" value="qtof"/>
940 <param name="formula" value=""/>
941 <param name="ions_enforced" value=""/>
942 <param name="candidates" value="5"/>
943 <param name="candidates_per_ion" value="-1"/>
944 <param name="elements_considered" value=""/>
945 <param name="elements_enforced" value=""/>
946 <param name="no_isotope_score" value="false"/>
947 <param name="no_isotope_filter" value="false"/>
948 <param name="ions_considered" value=""/>
949 <param name="db" value=""/>
950 </section>
951 <section name="fingerid">
952 <param name="candidates" value="10"/>
953 <param name="db" value="BIO"/>
954 </section>
955 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
956 <output name="ctd_out" ftype="xml">
957 <assert_contents>
958 <is_valid_xml/>
959 </assert_contents>
960 </output>
961 </test>
962 <!-- UTILS_AssayGeneratorMetabo_10 -->
963 <test expect_num_outputs="2">
964 <section name="adv_opts">
965 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
966 <param name="precursor_recalibration_window" value="0.01"/>
967 <param name="precursor_recalibration_window_unit" value="Da"/>
968 <param name="min_fragment_mz" value="100.0"/>
969 <param name="max_fragment_mz" value="900.0"/>
970 <param name="force" value="false"/>
971 <param name="test" value="true"/>
972 </section>
973 <conditional name="in_cond">
974 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
975 </conditional>
976 <conditional name="in_id_cond">
977 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
978 </conditional>
979 <param name="out_type" value="tsv"/>
980 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
981 <param name="fragment_annotation" value="sirius"/>
982 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
983 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
984 <param name="total_occurrence_filter" value="0.1"/>
985 <param name="fragment_annotation_score_threshold" value="0.8"/>
986 <param name="decoy_generation" value="false"/>
987 <param name="decoy_generation_method" value="original"/>
988 <param name="method" value="highest_intensity"/>
989 <param name="use_exact_mass" value="true"/>
990 <param name="exclude_ms2_precursor" value="false"/>
991 <param name="precursor_mz_distance" value="0.0001"/>
992 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
993 <param name="use_known_unknowns" value="false"/>
994 <param name="min_transitions" value="2"/>
995 <param name="max_transitions" value="3"/>
996 <param name="cosine_similarity_threshold" value="0.98"/>
997 <param name="transition_threshold" value="3.0"/>
998 <section name="deisotoping">
999 <param name="use_deisotoper" value="false"/>
1000 <param name="fragment_tolerance" value="1.0"/>
1001 <param name="fragment_unit" value="ppm"/>
1002 <param name="min_charge" value="1"/>
1003 <param name="max_charge" value="1"/>
1004 <param name="min_isopeaks" value="2"/>
1005 <param name="max_isopeaks" value="3"/>
1006 <param name="keep_only_deisotoped" value="false"/>
1007 <param name="annotate_charge" value="false"/>
1008 </section>
1009 <section name="preprocessing">
1010 <param name="filter_by_num_masstraces" value="1"/>
1011 <param name="precursor_mz_tolerance" value="10.0"/>
1012 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1013 <param name="precursor_rt_tolerance" value="5.0"/>
1014 <param name="isotope_pattern_iterations" value="3"/>
1015 <param name="feature_only" value="true"/>
1016 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1017 </section>
1018 <section name="project">
1019 <param name="processors" value="1"/>
1020 <param name="ignore_formula" value="false"/>
1021 <param name="q" value="false"/>
1022 </section>
1023 <section name="sirius">
1024 <param name="ppm_max" value="10.0"/>
1025 <param name="ppm_max_ms2" value="10.0"/>
1026 <param name="tree_timeout" value="0"/>
1027 <param name="compound_timeout" value="100"/>
1028 <param name="no_recalibration" value="false"/>
1029 <param name="profile" value="qtof"/>
1030 <param name="formula" value=""/>
1031 <param name="ions_enforced" value=""/>
1032 <param name="candidates" value="5"/>
1033 <param name="candidates_per_ion" value="-1"/>
1034 <param name="elements_considered" value=""/>
1035 <param name="elements_enforced" value=""/>
1036 <param name="no_isotope_score" value="false"/>
1037 <param name="no_isotope_filter" value="false"/>
1038 <param name="ions_considered" value=""/>
1039 <param name="db" value=""/>
1040 </section>
1041 <section name="fingerid">
1042 <param name="candidates" value="10"/>
1043 <param name="db" value="BIO"/>
1044 </section>
1045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1046 <output name="ctd_out" ftype="xml">
1047 <assert_contents>
1048 <is_valid_xml/>
1049 </assert_contents>
1050 </output>
1051 </test>
1052 <!-- UTILS_AssayGeneratorMetabo_11 -->
1053 <test expect_num_outputs="2">
1054 <section name="adv_opts">
1055 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1056 <param name="precursor_recalibration_window" value="0.01"/>
1057 <param name="precursor_recalibration_window_unit" value="Da"/>
1058 <param name="min_fragment_mz" value="100.0"/>
1059 <param name="max_fragment_mz" value="900.0"/>
1060 <param name="force" value="false"/>
1061 <param name="test" value="true"/>
1062 </section>
1063 <conditional name="in_cond">
1064 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
1065 </conditional>
1066 <conditional name="in_id_cond">
1067 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
1068 </conditional>
1069 <param name="out_type" value="tsv"/>
1070 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_decoy_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1071 <param name="fragment_annotation" value="sirius"/>
1072 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1073 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1074 <param name="total_occurrence_filter" value="0.1"/>
1075 <param name="fragment_annotation_score_threshold" value="0.8"/>
1076 <param name="decoy_generation" value="true"/>
1077 <param name="decoy_generation_method" value="original"/>
1078 <param name="method" value="highest_intensity"/>
1079 <param name="use_exact_mass" value="true"/>
1080 <param name="exclude_ms2_precursor" value="false"/>
1081 <param name="precursor_mz_distance" value="0.0001"/>
1082 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1083 <param name="use_known_unknowns" value="false"/>
1084 <param name="min_transitions" value="3"/>
1085 <param name="max_transitions" value="3"/>
1086 <param name="cosine_similarity_threshold" value="0.98"/>
1087 <param name="transition_threshold" value="3.0"/>
1088 <section name="deisotoping">
1089 <param name="use_deisotoper" value="false"/>
1090 <param name="fragment_tolerance" value="1.0"/>
1091 <param name="fragment_unit" value="ppm"/>
1092 <param name="min_charge" value="1"/>
1093 <param name="max_charge" value="1"/>
1094 <param name="min_isopeaks" value="2"/>
1095 <param name="max_isopeaks" value="3"/>
1096 <param name="keep_only_deisotoped" value="false"/>
1097 <param name="annotate_charge" value="false"/>
1098 </section>
1099 <section name="preprocessing">
1100 <param name="filter_by_num_masstraces" value="1"/>
1101 <param name="precursor_mz_tolerance" value="10.0"/>
1102 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1103 <param name="precursor_rt_tolerance" value="5.0"/>
1104 <param name="isotope_pattern_iterations" value="3"/>
1105 <param name="feature_only" value="true"/>
1106 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1107 </section>
1108 <section name="project">
1109 <param name="processors" value="1"/>
1110 <param name="ignore_formula" value="false"/>
1111 <param name="q" value="false"/>
1112 </section>
1113 <section name="sirius">
1114 <param name="ppm_max" value="10.0"/>
1115 <param name="ppm_max_ms2" value="10.0"/>
1116 <param name="tree_timeout" value="0"/>
1117 <param name="compound_timeout" value="100"/>
1118 <param name="no_recalibration" value="false"/>
1119 <param name="profile" value="qtof"/>
1120 <param name="formula" value=""/>
1121 <param name="ions_enforced" value=""/>
1122 <param name="candidates" value="5"/>
1123 <param name="candidates_per_ion" value="-1"/>
1124 <param name="elements_considered" value=""/>
1125 <param name="elements_enforced" value=""/>
1126 <param name="no_isotope_score" value="false"/>
1127 <param name="no_isotope_filter" value="false"/>
1128 <param name="ions_considered" value=""/>
1129 <param name="db" value=""/>
1130 </section>
1131 <section name="fingerid">
1132 <param name="candidates" value="10"/>
1133 <param name="db" value="BIO"/>
1134 </section>
1135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1136 <output name="ctd_out" ftype="xml">
1137 <assert_contents>
1138 <is_valid_xml/>
1139 </assert_contents>
1140 </output>
1141 </test>
1142 <!-- UTILS_AssayGeneratorMetabo_12 -->
1143 <test expect_num_outputs="2">
1144 <section name="adv_opts">
1145 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1146 <param name="precursor_recalibration_window" value="0.01"/>
1147 <param name="precursor_recalibration_window_unit" value="Da"/>
1148 <param name="min_fragment_mz" value="100.0"/>
1149 <param name="max_fragment_mz" value="900.0"/>
1150 <param name="force" value="false"/>
1151 <param name="test" value="true"/>
1152 </section>
1153 <conditional name="in_cond">
1154 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
1155 </conditional>
1156 <conditional name="in_id_cond">
1157 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
1158 </conditional>
1159 <param name="out_type" value="tsv"/>
1160 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_original.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1161 <param name="fragment_annotation" value="sirius"/>
1162 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1163 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1164 <param name="total_occurrence_filter" value="0.1"/>
1165 <param name="fragment_annotation_score_threshold" value="0.8"/>
1166 <param name="decoy_generation" value="true"/>
1167 <param name="decoy_generation_method" value="original"/>
1168 <param name="method" value="highest_intensity"/>
1169 <param name="use_exact_mass" value="true"/>
1170 <param name="exclude_ms2_precursor" value="false"/>
1171 <param name="precursor_mz_distance" value="0.0001"/>
1172 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1173 <param name="use_known_unknowns" value="false"/>
1174 <param name="min_transitions" value="1"/>
1175 <param name="max_transitions" value="3"/>
1176 <param name="cosine_similarity_threshold" value="0.98"/>
1177 <param name="transition_threshold" value="3.0"/>
1178 <section name="deisotoping">
1179 <param name="use_deisotoper" value="false"/>
1180 <param name="fragment_tolerance" value="1.0"/>
1181 <param name="fragment_unit" value="ppm"/>
1182 <param name="min_charge" value="1"/>
1183 <param name="max_charge" value="1"/>
1184 <param name="min_isopeaks" value="2"/>
1185 <param name="max_isopeaks" value="3"/>
1186 <param name="keep_only_deisotoped" value="false"/>
1187 <param name="annotate_charge" value="false"/>
1188 </section>
1189 <section name="preprocessing">
1190 <param name="filter_by_num_masstraces" value="1"/>
1191 <param name="precursor_mz_tolerance" value="10.0"/>
1192 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1193 <param name="precursor_rt_tolerance" value="5.0"/>
1194 <param name="isotope_pattern_iterations" value="3"/>
1195 <param name="feature_only" value="true"/>
1196 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1197 </section>
1198 <section name="project">
1199 <param name="processors" value="1"/>
1200 <param name="ignore_formula" value="false"/>
1201 <param name="q" value="false"/>
1202 </section>
1203 <section name="sirius">
1204 <param name="ppm_max" value="10.0"/>
1205 <param name="ppm_max_ms2" value="10.0"/>
1206 <param name="tree_timeout" value="0"/>
1207 <param name="compound_timeout" value="100"/>
1208 <param name="no_recalibration" value="false"/>
1209 <param name="profile" value="qtof"/>
1210 <param name="formula" value=""/>
1211 <param name="ions_enforced" value=""/>
1212 <param name="candidates" value="5"/>
1213 <param name="candidates_per_ion" value="-1"/>
1214 <param name="elements_considered" value=""/>
1215 <param name="elements_enforced" value=""/>
1216 <param name="no_isotope_score" value="false"/>
1217 <param name="no_isotope_filter" value="false"/>
1218 <param name="ions_considered" value=""/>
1219 <param name="db" value=""/>
1220 </section>
1221 <section name="fingerid">
1222 <param name="candidates" value="10"/>
1223 <param name="db" value="BIO"/>
1224 </section>
1225 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1226 <output name="ctd_out" ftype="xml">
1227 <assert_contents>
1228 <is_valid_xml/>
1229 </assert_contents>
1230 </output>
1231 </test>
1232 <!-- UTILS_AssayGeneratorMetabo_13 -->
1233 <test expect_num_outputs="2">
1234 <section name="adv_opts">
1235 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1236 <param name="precursor_recalibration_window" value="0.01"/>
1237 <param name="precursor_recalibration_window_unit" value="Da"/>
1238 <param name="min_fragment_mz" value="100.0"/>
1239 <param name="max_fragment_mz" value="900.0"/>
1240 <param name="force" value="false"/>
1241 <param name="test" value="true"/>
1242 </section>
1243 <conditional name="in_cond">
1244 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
1245 </conditional>
1246 <conditional name="in_id_cond">
1247 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
1248 </conditional>
1249 <param name="out_type" value="tsv"/>
1250 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_resolve_overlap.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1251 <param name="fragment_annotation" value="sirius"/>
1252 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1253 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1254 <param name="total_occurrence_filter" value="0.1"/>
1255 <param name="fragment_annotation_score_threshold" value="0.8"/>
1256 <param name="decoy_generation" value="true"/>
1257 <param name="decoy_generation_method" value="resolve_overlap"/>
1258 <param name="method" value="highest_intensity"/>
1259 <param name="use_exact_mass" value="true"/>
1260 <param name="exclude_ms2_precursor" value="false"/>
1261 <param name="precursor_mz_distance" value="0.0001"/>
1262 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1263 <param name="use_known_unknowns" value="false"/>
1264 <param name="min_transitions" value="1"/>
1265 <param name="max_transitions" value="3"/>
1266 <param name="cosine_similarity_threshold" value="0.98"/>
1267 <param name="transition_threshold" value="3.0"/>
1268 <section name="deisotoping">
1269 <param name="use_deisotoper" value="false"/>
1270 <param name="fragment_tolerance" value="1.0"/>
1271 <param name="fragment_unit" value="ppm"/>
1272 <param name="min_charge" value="1"/>
1273 <param name="max_charge" value="1"/>
1274 <param name="min_isopeaks" value="2"/>
1275 <param name="max_isopeaks" value="3"/>
1276 <param name="keep_only_deisotoped" value="false"/>
1277 <param name="annotate_charge" value="false"/>
1278 </section>
1279 <section name="preprocessing">
1280 <param name="filter_by_num_masstraces" value="1"/>
1281 <param name="precursor_mz_tolerance" value="10.0"/>
1282 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1283 <param name="precursor_rt_tolerance" value="5.0"/>
1284 <param name="isotope_pattern_iterations" value="3"/>
1285 <param name="feature_only" value="true"/>
1286 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1287 </section>
1288 <section name="project">
1289 <param name="processors" value="1"/>
1290 <param name="ignore_formula" value="false"/>
1291 <param name="q" value="false"/>
1292 </section>
1293 <section name="sirius">
1294 <param name="ppm_max" value="10.0"/>
1295 <param name="ppm_max_ms2" value="10.0"/>
1296 <param name="tree_timeout" value="0"/>
1297 <param name="compound_timeout" value="100"/>
1298 <param name="no_recalibration" value="false"/>
1299 <param name="profile" value="qtof"/>
1300 <param name="formula" value=""/>
1301 <param name="ions_enforced" value=""/>
1302 <param name="candidates" value="5"/>
1303 <param name="candidates_per_ion" value="-1"/>
1304 <param name="elements_considered" value=""/>
1305 <param name="elements_enforced" value=""/>
1306 <param name="no_isotope_score" value="false"/>
1307 <param name="no_isotope_filter" value="false"/>
1308 <param name="ions_considered" value=""/>
1309 <param name="db" value=""/>
1310 </section>
1311 <section name="fingerid">
1312 <param name="candidates" value="10"/>
1313 <param name="db" value="BIO"/>
1314 </section>
1315 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1316 <output name="ctd_out" ftype="xml">
1317 <assert_contents>
1318 <is_valid_xml/>
1319 </assert_contents>
1320 </output>
1321 </test>
1322 <!-- UTILS_AssayGeneratorMetabo_14 -->
1323 <test expect_num_outputs="2">
1324 <section name="adv_opts">
1325 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1326 <param name="precursor_recalibration_window" value="0.01"/>
1327 <param name="precursor_recalibration_window_unit" value="Da"/>
1328 <param name="min_fragment_mz" value="100.0"/>
1329 <param name="max_fragment_mz" value="900.0"/>
1330 <param name="force" value="false"/>
1331 <param name="test" value="true"/>
1332 </section>
1333 <conditional name="in_cond">
1334 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
1335 </conditional>
1336 <conditional name="in_id_cond">
1337 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
1338 </conditional>
1339 <param name="out_type" value="tsv"/>
1340 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_add_shift.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1341 <param name="fragment_annotation" value="sirius"/>
1342 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1343 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1344 <param name="total_occurrence_filter" value="0.1"/>
1345 <param name="fragment_annotation_score_threshold" value="0.8"/>
1346 <param name="decoy_generation" value="true"/>
1347 <param name="decoy_generation_method" value="add_shift"/>
1348 <param name="method" value="highest_intensity"/>
1349 <param name="use_exact_mass" value="true"/>
1350 <param name="exclude_ms2_precursor" value="false"/>
1351 <param name="precursor_mz_distance" value="0.0001"/>
1352 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1353 <param name="use_known_unknowns" value="false"/>
1354 <param name="min_transitions" value="1"/>
1355 <param name="max_transitions" value="3"/>
1356 <param name="cosine_similarity_threshold" value="0.98"/>
1357 <param name="transition_threshold" value="3.0"/>
1358 <section name="deisotoping">
1359 <param name="use_deisotoper" value="false"/>
1360 <param name="fragment_tolerance" value="1.0"/>
1361 <param name="fragment_unit" value="ppm"/>
1362 <param name="min_charge" value="1"/>
1363 <param name="max_charge" value="1"/>
1364 <param name="min_isopeaks" value="2"/>
1365 <param name="max_isopeaks" value="3"/>
1366 <param name="keep_only_deisotoped" value="false"/>
1367 <param name="annotate_charge" value="false"/>
1368 </section>
1369 <section name="preprocessing">
1370 <param name="filter_by_num_masstraces" value="1"/>
1371 <param name="precursor_mz_tolerance" value="10.0"/>
1372 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1373 <param name="precursor_rt_tolerance" value="5.0"/>
1374 <param name="isotope_pattern_iterations" value="3"/>
1375 <param name="feature_only" value="true"/>
1376 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1377 </section>
1378 <section name="project">
1379 <param name="processors" value="1"/>
1380 <param name="ignore_formula" value="false"/>
1381 <param name="q" value="false"/>
1382 </section>
1383 <section name="sirius">
1384 <param name="ppm_max" value="10.0"/>
1385 <param name="ppm_max_ms2" value="10.0"/>
1386 <param name="tree_timeout" value="0"/>
1387 <param name="compound_timeout" value="100"/>
1388 <param name="no_recalibration" value="false"/>
1389 <param name="profile" value="qtof"/>
1390 <param name="formula" value=""/>
1391 <param name="ions_enforced" value=""/>
1392 <param name="candidates" value="5"/>
1393 <param name="candidates_per_ion" value="-1"/>
1394 <param name="elements_considered" value=""/>
1395 <param name="elements_enforced" value=""/>
1396 <param name="no_isotope_score" value="false"/>
1397 <param name="no_isotope_filter" value="false"/>
1398 <param name="ions_considered" value=""/>
1399 <param name="db" value=""/>
1400 </section>
1401 <section name="fingerid">
1402 <param name="candidates" value="10"/>
1403 <param name="db" value="BIO"/>
1404 </section>
1405 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1406 <output name="ctd_out" ftype="xml">
1407 <assert_contents>
1408 <is_valid_xml/>
1409 </assert_contents>
1410 </output>
1411 </test>
1412 <!-- UTILS_AssayGeneratorMetabo_15 -->
1413 <test expect_num_outputs="2">
1414 <section name="adv_opts">
1415 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1416 <param name="precursor_recalibration_window" value="0.01"/>
1417 <param name="precursor_recalibration_window_unit" value="Da"/>
1418 <param name="min_fragment_mz" value="100.0"/>
1419 <param name="max_fragment_mz" value="900.0"/>
1420 <param name="force" value="false"/>
1421 <param name="test" value="true"/>
1422 </section>
1423 <conditional name="in_cond">
1424 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
1425 </conditional>
1426 <conditional name="in_id_cond">
1427 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
1428 </conditional>
1429 <param name="out_type" value="tsv"/>
1430 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1431 <param name="fragment_annotation" value="sirius"/>
1432 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1433 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1434 <param name="total_occurrence_filter" value="0.1"/>
1435 <param name="fragment_annotation_score_threshold" value="0.8"/>
1436 <param name="decoy_generation" value="true"/>
1437 <param name="decoy_generation_method" value="both"/>
1438 <param name="method" value="highest_intensity"/>
1439 <param name="use_exact_mass" value="true"/>
1440 <param name="exclude_ms2_precursor" value="false"/>
1441 <param name="precursor_mz_distance" value="0.0001"/>
1442 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1443 <param name="use_known_unknowns" value="false"/>
1444 <param name="min_transitions" value="1"/>
1445 <param name="max_transitions" value="3"/>
1446 <param name="cosine_similarity_threshold" value="0.98"/>
1447 <param name="transition_threshold" value="3.0"/>
1448 <section name="deisotoping">
1449 <param name="use_deisotoper" value="false"/>
1450 <param name="fragment_tolerance" value="1.0"/>
1451 <param name="fragment_unit" value="ppm"/>
1452 <param name="min_charge" value="1"/>
1453 <param name="max_charge" value="1"/>
1454 <param name="min_isopeaks" value="2"/>
1455 <param name="max_isopeaks" value="3"/>
1456 <param name="keep_only_deisotoped" value="false"/>
1457 <param name="annotate_charge" value="false"/>
1458 </section>
1459 <section name="preprocessing">
1460 <param name="filter_by_num_masstraces" value="1"/>
1461 <param name="precursor_mz_tolerance" value="10.0"/>
1462 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1463 <param name="precursor_rt_tolerance" value="5.0"/>
1464 <param name="isotope_pattern_iterations" value="3"/>
1465 <param name="feature_only" value="true"/>
1466 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1467 </section>
1468 <section name="project">
1469 <param name="processors" value="1"/>
1470 <param name="ignore_formula" value="false"/>
1471 <param name="q" value="false"/>
1472 </section>
1473 <section name="sirius">
1474 <param name="ppm_max" value="10.0"/>
1475 <param name="ppm_max_ms2" value="10.0"/>
1476 <param name="tree_timeout" value="0"/>
1477 <param name="compound_timeout" value="100"/>
1478 <param name="no_recalibration" value="false"/>
1479 <param name="profile" value="qtof"/>
1480 <param name="formula" value=""/>
1481 <param name="ions_enforced" value=""/>
1482 <param name="candidates" value="5"/>
1483 <param name="candidates_per_ion" value="-1"/>
1484 <param name="elements_considered" value=""/>
1485 <param name="elements_enforced" value=""/>
1486 <param name="no_isotope_score" value="false"/>
1487 <param name="no_isotope_filter" value="false"/>
1488 <param name="ions_considered" value=""/>
1489 <param name="db" value=""/>
1490 </section>
1491 <section name="fingerid">
1492 <param name="candidates" value="10"/>
1493 <param name="db" value="BIO"/>
1494 </section>
1495 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1496 <output name="ctd_out" ftype="xml">
1497 <assert_contents>
1498 <is_valid_xml/>
1499 </assert_contents>
1500 </output>
1501 </test>
1502 <!-- UTILS_AssayGeneratorMetabo_16 -->
1503 <test expect_num_outputs="2">
1504 <section name="adv_opts">
1505 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
1506 <param name="precursor_recalibration_window" value="0.01"/>
1507 <param name="precursor_recalibration_window_unit" value="Da"/>
1508 <param name="min_fragment_mz" value="100.0"/>
1509 <param name="max_fragment_mz" value="900.0"/>
1510 <param name="force" value="false"/>
1511 <param name="test" value="true"/>
1512 </section>
1513 <conditional name="in_cond">
1514 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
1515 </conditional>
1516 <conditional name="in_id_cond">
1517 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
1518 </conditional>
1519 <param name="out_type" value="tsv"/>
1520 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both_multids.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1521 <param name="fragment_annotation" value="sirius"/>
1522 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1523 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1524 <param name="total_occurrence_filter" value="0.1"/>
1525 <param name="fragment_annotation_score_threshold" value="0.8"/>
1526 <param name="decoy_generation" value="true"/>
1527 <param name="decoy_generation_method" value="both"/>
1528 <param name="method" value="highest_intensity"/>
1529 <param name="use_exact_mass" value="true"/>
1530 <param name="exclude_ms2_precursor" value="false"/>
1531 <param name="precursor_mz_distance" value="0.0001"/>
1532 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1533 <param name="use_known_unknowns" value="false"/>
1534 <param name="min_transitions" value="1"/>
1535 <param name="max_transitions" value="3"/>
1536 <param name="cosine_similarity_threshold" value="0.98"/>
1537 <param name="transition_threshold" value="3.0"/>
1538 <section name="deisotoping">
1539 <param name="use_deisotoper" value="false"/>
1540 <param name="fragment_tolerance" value="1.0"/>
1541 <param name="fragment_unit" value="ppm"/>
1542 <param name="min_charge" value="1"/>
1543 <param name="max_charge" value="1"/>
1544 <param name="min_isopeaks" value="2"/>
1545 <param name="max_isopeaks" value="3"/>
1546 <param name="keep_only_deisotoped" value="false"/>
1547 <param name="annotate_charge" value="false"/>
1548 </section>
1549 <section name="preprocessing">
1550 <param name="filter_by_num_masstraces" value="1"/>
1551 <param name="precursor_mz_tolerance" value="10.0"/>
1552 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1553 <param name="precursor_rt_tolerance" value="5.0"/>
1554 <param name="isotope_pattern_iterations" value="3"/>
1555 <param name="feature_only" value="true"/>
1556 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1557 </section>
1558 <section name="project">
1559 <param name="processors" value="1"/>
1560 <param name="ignore_formula" value="false"/>
1561 <param name="q" value="false"/>
1562 </section>
1563 <section name="sirius">
1564 <param name="ppm_max" value="10.0"/>
1565 <param name="ppm_max_ms2" value="10.0"/>
1566 <param name="tree_timeout" value="0"/>
1567 <param name="compound_timeout" value="100"/>
1568 <param name="no_recalibration" value="false"/>
1569 <param name="profile" value="qtof"/>
1570 <param name="formula" value=""/>
1571 <param name="ions_enforced" value=""/>
1572 <param name="candidates" value="5"/>
1573 <param name="candidates_per_ion" value="-1"/>
1574 <param name="elements_considered" value=""/>
1575 <param name="elements_enforced" value=""/>
1576 <param name="no_isotope_score" value="false"/>
1577 <param name="no_isotope_filter" value="false"/>
1578 <param name="ions_considered" value=""/>
1579 <param name="db" value=""/>
1580 </section>
1581 <section name="fingerid">
1582 <param name="candidates" value="10"/>
1583 <param name="db" value="BIO"/>
1584 </section>
1585 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1586 <output name="ctd_out" ftype="xml">
1587 <assert_contents>
1588 <is_valid_xml/>
1589 </assert_contents>
1590 </output>
1591 </test>
1592 <!-- UTILS_AssayGeneratorMetabo_17 -->
1593 <test expect_num_outputs="2">
1594 <section name="adv_opts">
1595 <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
1596 <param name="precursor_recalibration_window" value="0.01"/>
1597 <param name="precursor_recalibration_window_unit" value="Da"/>
1598 <param name="min_fragment_mz" value="0.0"/>
1599 <param name="max_fragment_mz" value="2000.0"/>
1600 <param name="force" value="false"/>
1601 <param name="test" value="true"/>
1602 </section>
1603 <conditional name="in_cond">
1604 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
1605 </conditional>
1606 <conditional name="in_id_cond">
1607 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
1608 </conditional>
1609 <param name="out_type" value="tsv"/>
1610 <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1611 <param name="fragment_annotation" value="sirius"/>
1612 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1613 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1614 <param name="total_occurrence_filter" value="0.8"/>
1615 <param name="fragment_annotation_score_threshold" value="0.8"/>
1616 <param name="decoy_generation" value="true"/>
1617 <param name="decoy_generation_method" value="both"/>
1618 <param name="method" value="highest_intensity"/>
1619 <param name="use_exact_mass" value="true"/>
1620 <param name="exclude_ms2_precursor" value="false"/>
1621 <param name="precursor_mz_distance" value="0.0001"/>
1622 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1623 <param name="use_known_unknowns" value="false"/>
1624 <param name="min_transitions" value="1"/>
1625 <param name="max_transitions" value="6"/>
1626 <param name="cosine_similarity_threshold" value="0.98"/>
1627 <param name="transition_threshold" value="3.0"/>
1628 <section name="deisotoping">
1629 <param name="use_deisotoper" value="false"/>
1630 <param name="fragment_tolerance" value="1.0"/>
1631 <param name="fragment_unit" value="ppm"/>
1632 <param name="min_charge" value="1"/>
1633 <param name="max_charge" value="1"/>
1634 <param name="min_isopeaks" value="2"/>
1635 <param name="max_isopeaks" value="3"/>
1636 <param name="keep_only_deisotoped" value="false"/>
1637 <param name="annotate_charge" value="false"/>
1638 </section>
1639 <section name="preprocessing">
1640 <param name="filter_by_num_masstraces" value="1"/>
1641 <param name="precursor_mz_tolerance" value="10.0"/>
1642 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1643 <param name="precursor_rt_tolerance" value="5.0"/>
1644 <param name="isotope_pattern_iterations" value="3"/>
1645 <param name="feature_only" value="true"/>
1646 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1647 </section>
1648 <section name="project">
1649 <param name="processors" value="1"/>
1650 <param name="ignore_formula" value="false"/>
1651 <param name="q" value="false"/>
1652 </section>
1653 <section name="sirius">
1654 <param name="ppm_max" value="10.0"/>
1655 <param name="ppm_max_ms2" value="10.0"/>
1656 <param name="tree_timeout" value="0"/>
1657 <param name="compound_timeout" value="100"/>
1658 <param name="no_recalibration" value="false"/>
1659 <param name="profile" value="qtof"/>
1660 <param name="formula" value=""/>
1661 <param name="ions_enforced" value=""/>
1662 <param name="candidates" value="5"/>
1663 <param name="candidates_per_ion" value="-1"/>
1664 <param name="elements_considered" value=""/>
1665 <param name="elements_enforced" value=""/>
1666 <param name="no_isotope_score" value="false"/>
1667 <param name="no_isotope_filter" value="false"/>
1668 <param name="ions_considered" value=""/>
1669 <param name="db" value=""/>
1670 </section>
1671 <section name="fingerid">
1672 <param name="candidates" value="10"/>
1673 <param name="db" value="BIO"/>
1674 </section>
1675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1676 <output name="ctd_out" ftype="xml">
1677 <assert_contents>
1678 <is_valid_xml/>
1679 </assert_contents>
1680 </output>
1681 </test>
1682 <!-- UTILS_AssayGeneratorMetabo_18 -->
1683 <test expect_num_outputs="2">
1684 <section name="adv_opts">
1685 <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
1686 <param name="precursor_recalibration_window" value="0.01"/>
1687 <param name="precursor_recalibration_window_unit" value="Da"/>
1688 <param name="min_fragment_mz" value="0.0"/>
1689 <param name="max_fragment_mz" value="2000.0"/>
1690 <param name="force" value="false"/>
1691 <param name="test" value="true"/>
1692 </section>
1693 <conditional name="in_cond">
1694 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
1695 </conditional>
1696 <conditional name="in_id_cond">
1697 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
1698 </conditional>
1699 <param name="out_type" value="tsv"/>
1700 <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_moladd_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
1701 <param name="fragment_annotation" value="sirius"/>
1702 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
1703 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
1704 <param name="total_occurrence_filter" value="0.1"/>
1705 <param name="fragment_annotation_score_threshold" value="0.8"/>
1706 <param name="decoy_generation" value="true"/>
1707 <param name="decoy_generation_method" value="both"/>
1708 <param name="method" value="highest_intensity"/>
1709 <param name="use_exact_mass" value="true"/>
1710 <param name="exclude_ms2_precursor" value="false"/>
1711 <param name="precursor_mz_distance" value="0.0001"/>
1712 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
1713 <param name="use_known_unknowns" value="false"/>
1714 <param name="min_transitions" value="1"/>
1715 <param name="max_transitions" value="6"/>
1716 <param name="cosine_similarity_threshold" value="0.98"/>
1717 <param name="transition_threshold" value="3.0"/>
1718 <section name="deisotoping">
1719 <param name="use_deisotoper" value="false"/>
1720 <param name="fragment_tolerance" value="1.0"/>
1721 <param name="fragment_unit" value="ppm"/>
1722 <param name="min_charge" value="1"/>
1723 <param name="max_charge" value="1"/>
1724 <param name="min_isopeaks" value="2"/>
1725 <param name="max_isopeaks" value="3"/>
1726 <param name="keep_only_deisotoped" value="false"/>
1727 <param name="annotate_charge" value="false"/>
1728 </section>
1729 <section name="preprocessing">
1730 <param name="filter_by_num_masstraces" value="1"/>
1731 <param name="precursor_mz_tolerance" value="10.0"/>
1732 <param name="precursor_mz_tolerance_unit" value="ppm"/>
1733 <param name="precursor_rt_tolerance" value="5.0"/>
1734 <param name="isotope_pattern_iterations" value="3"/>
1735 <param name="feature_only" value="true"/>
1736 <param name="no_masstrace_info_isotope_pattern" value="false"/>
1737 </section>
1738 <section name="project">
1739 <param name="processors" value="1"/>
1740 <param name="ignore_formula" value="false"/>
1741 <param name="q" value="false"/>
1742 </section>
1743 <section name="sirius">
1744 <param name="ppm_max" value="10.0"/>
1745 <param name="ppm_max_ms2" value="10.0"/>
1746 <param name="tree_timeout" value="0"/>
1747 <param name="compound_timeout" value="100"/>
1748 <param name="no_recalibration" value="false"/>
1749 <param name="profile" value="qtof"/>
1750 <param name="formula" value=""/>
1751 <param name="ions_enforced" value=""/>
1752 <param name="candidates" value="5"/>
1753 <param name="candidates_per_ion" value="-1"/>
1754 <param name="elements_considered" value=""/>
1755 <param name="elements_enforced" value=""/>
1756 <param name="no_isotope_score" value="false"/>
1757 <param name="no_isotope_filter" value="false"/>
1758 <param name="ions_considered" value=""/>
1759 <param name="db" value=""/>
1760 </section>
1761 <section name="fingerid">
1762 <param name="candidates" value="10"/>
1763 <param name="db" value="BIO"/>
1764 </section>
1765 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1766 <output name="ctd_out" ftype="xml">
1767 <assert_contents>
1768 <is_valid_xml/>
1769 </assert_contents>
1770 </output>
1771 </test> 719 </test>
1772 </tests> 720 </tests>
1773 <help><![CDATA[Assay library generation from DDA data (Metabolomics) 721 <help><![CDATA[Assay library generation from DDA data (Metabolomics)
1774 722
1775 723
1776 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AssayGeneratorMetabo.html]]></help> 724 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_AssayGeneratorMetabo.html]]></help>
1777 <expand macro="references"/> 725 <expand macro="references"/>
1778 </tool> 726 </tool>