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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:41:27 +0000
parents 532cf3ddcc91
children
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16:532cf3ddcc91 17:31e674c86840
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: [Metabolite Identification]-->
4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Match MS signals to molecules from a database by mass.</description> 4 <description>Match MS signals to molecules from a database by mass</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">AccurateMassSearch</token> 6 <token name="@EXECUTABLE@">AccurateMassSearch</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir out_annotation && 20 mkdir out_annotation &&
22 #end if 21 #end if
23 #if $positive_adducts: 22 #if $positive_adducts:
24 mkdir positive_adducts && 23 mkdir positive_adducts &&
25 ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' && 24 cp '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
26 #end if 25 #end if
27 #if $negative_adducts: 26 #if $negative_adducts:
28 mkdir negative_adducts && 27 mkdir negative_adducts &&
29 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' && 28 cp '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
30 #end if 29 #end if
31 #if $db.mapping_cond.mapping: 30 #if $db.mapping_cond.mapping:
32 mkdir db.mapping_cond.mapping && 31 mkdir db.mapping_cond.mapping &&
33 #if $db.mapping_cond.mapping_select == "no" 32 #if $db.mapping_cond.mapping_select == "no"
34 mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} && 33 mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} &&
35 ${' '.join(["ln -s '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])} 34 ${' '.join(["cp '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
36 #else 35 #else
37 ln -s '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' && 36 cp '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' &&
38 #end if 37 #end if
39 #end if 38 #end if
40 #if $db.struct_cond.struct: 39 #if $db.struct_cond.struct:
41 mkdir db.struct_cond.struct && 40 mkdir db.struct_cond.struct &&
42 #if $db.struct_cond.struct_select == "no" 41 #if $db.struct_cond.struct_select == "no"
43 mkdir ${' '.join(["'db.struct_cond.struct/%s'" % (i) for i, f in enumerate($db.struct_cond.struct) if f])} && 42 mkdir ${' '.join(["'db.struct_cond.struct/%s'" % (i) for i, f in enumerate($db.struct_cond.struct) if f])} &&
44 ${' '.join(["ln -s '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])} 43 ${' '.join(["cp '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
45 #else 44 #else
46 ln -s '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' && 45 cp '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' &&
47 #end if 46 #end if
48 #end if 47 #end if
49 48
50 ## Main program call 49 ## Main program call
51 50
100 <configfiles> 99 <configfiles>
101 <inputs name="args_json" data_style="paths"/> 100 <inputs name="args_json" data_style="paths"/>
102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 101 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
103 </configfiles> 102 </configfiles>
104 <inputs> 103 <inputs>
105 <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/> 104 <param argument="-in" type="data" format="consensusxml,featurexml" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
106 <param name="out_annotation_type" type="select" optional="false" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)"> 105 <param name="out_annotation_type" type="select" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)">
107 <option value="featureXML">featurexml</option> 106 <option value="featureXML">featurexml</option>
108 <option value="consensusXML">consensusxml</option> 107 <option value="consensusXML">consensusxml</option>
109 <option value="oms">sqlite (oms)</option> 108 <option value="oms">sqlite (oms)</option>
110 </param> 109 </param>
111 <param argument="-positive_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential positive adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/> 110 <param argument="-positive_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential positive adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
118 </param> 117 </param>
119 <when value="no"> 118 <when value="no">
120 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> 119 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
121 </when> 120 </when>
122 <when value="yes"> 121 <when value="yes">
123 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> 122 <param name="mapping" argument="-db:mapping" type="data" format="tabular" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
124 </when> 123 </when>
125 </conditional> 124 </conditional>
126 <conditional name="struct_cond"> 125 <conditional name="struct_cond">
127 <param name="struct_select" type="select" label="Run tool in batch mode for -struct"> 126 <param name="struct_select" type="select" label="Run tool in batch mode for -struct">
128 <option value="no">No: process all datasets jointly</option> 127 <option value="no">No: process all datasets jointly</option>
130 </param> 129 </param>
131 <when value="no"> 130 <when value="no">
132 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> 131 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
133 </when> 132 </when>
134 <when value="yes"> 133 <when value="yes">
135 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/> 134 <param name="struct" argument="-db:struct" type="data" format="tabular" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
136 </when> 135 </when>
137 </conditional> 136 </conditional>
138 </section> 137 </section>
139 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 138 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
140 <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/> 139 <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
141 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help=""> 140 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" label="Unit of mass error (ppm or Da)" help="">
142 <option value="ppm" selected="true">ppm</option> 141 <option value="ppm" selected="true">ppm</option>
143 <option value="Da">Da</option> 142 <option value="Da">Da</option>
144 <expand macro="list_string_san" name="mass_error_unit"/> 143 <expand macro="list_string_san" name="mass_error_unit"/>
145 </param> 144 </param>
146 <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error"> 145 <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
147 <option value="positive" selected="true">positive</option> 146 <option value="positive" selected="true">positive</option>
148 <option value="negative">negative</option> 147 <option value="negative">negative</option>
149 <option value="auto">auto</option> 148 <option value="auto">auto</option>
150 <expand macro="list_string_san" name="ionization_mode"/> 149 <expand macro="list_string_san" name="ionization_mode"/>
151 </param> 150 </param>
152 <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/> 151 <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
153 <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/> 152 <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
154 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/> 153 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/>
155 <param name="id_format" argument="-algorithm:id_format" type="select" optional="true" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help=""> 154 <param name="id_format" argument="-algorithm:id_format" type="select" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
156 <option value="legacy" selected="true">legacy</option> 155 <option value="legacy" selected="true">legacy</option>
157 <option value="ID">ID</option> 156 <option value="ID">ID</option>
158 <expand macro="list_string_san" name="id_format"/> 157 <expand macro="list_string_san" name="id_format"/>
159 </param> 158 </param>
160 <section name="mzTab" title="" help="" expanded="false"> 159 <section name="mzTab" title="" help="" expanded="false">
161 <param name="exportIsotopeIntensities" argument="-algorithm:mzTab:exportIsotopeIntensities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)" help=""/> 160 <param name="exportIsotopeIntensities" argument="-algorithm:mzTab:exportIsotopeIntensities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)" help=""/>
162 </section> 161 </section>
163 </section> 162 </section>
164 <expand macro="adv_opts_macro"> 163 <expand macro="adv_opts_macro">
165 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 164 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
166 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 165 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
167 <expand macro="list_string_san" name="test"/> 166 <expand macro="list_string_san" name="test"/>
168 </param> 167 </param>
169 </expand> 168 </expand>
170 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 169 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
171 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option> 170 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option>
183 </data> 182 </data>
184 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 183 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
185 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 184 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
186 </data> 185 </data>
187 </outputs> 186 </outputs>
188 <tests><!-- UTILS_AccurateMassSearch_1 --> 187 <tests>
188 <!-- TOPP_AccurateMassSearch_1 -->
189 <test expect_num_outputs="2"> 189 <test expect_num_outputs="2">
190 <section name="adv_opts"> 190 <section name="adv_opts">
191 <param name="force" value="false"/> 191 <param name="force" value="false"/>
192 <param name="test" value="true"/> 192 <param name="test" value="true"/>
193 </section> 193 </section>
194 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> 194 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
195 <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 195 <output name="out" value="AccurateMassSearch_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
196 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> 196 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
197 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> 197 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
198 <section name="db"> 198 <section name="db">
199 <conditional name="mapping_cond"> 199 <conditional name="mapping_cond">
200 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> 200 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
219 <output name="ctd_out" ftype="xml"> 219 <output name="ctd_out" ftype="xml">
220 <assert_contents> 220 <assert_contents>
221 <is_valid_xml/> 221 <is_valid_xml/>
222 </assert_contents> 222 </assert_contents>
223 </output> 223 </output>
224 <assert_stdout>
225 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
226 </assert_stdout>
224 </test> 227 </test>
225 <!-- UTILS_AccurateMassSearch_2 --> 228 <!-- TOPP_AccurateMassSearch_2 -->
226 <test expect_num_outputs="3"> 229 <test expect_num_outputs="3">
227 <section name="adv_opts"> 230 <section name="adv_opts">
228 <param name="force" value="false"/> 231 <param name="force" value="false"/>
229 <param name="test" value="true"/> 232 <param name="test" value="true"/>
230 </section> 233 </section>
231 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> 234 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
232 <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 235 <output name="out" value="AccurateMassSearch_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
233 <param name="out_annotation_type" value="featureXML"/> 236 <param name="out_annotation_type" value="featureXML"/>
234 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 237 <output name="out_annotation" value="AccurateMassSearch_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
235 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> 238 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
236 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> 239 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
237 <section name="db"> 240 <section name="db">
238 <conditional name="mapping_cond"> 241 <conditional name="mapping_cond">
239 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> 242 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
258 <output name="ctd_out" ftype="xml"> 261 <output name="ctd_out" ftype="xml">
259 <assert_contents> 262 <assert_contents>
260 <is_valid_xml/> 263 <is_valid_xml/>
261 </assert_contents> 264 </assert_contents>
262 </output> 265 </output>
266 <assert_stdout>
267 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
268 </assert_stdout>
263 </test> 269 </test>
264 <!-- UTILS_AccurateMassSearch_3 --> 270 <!-- TOPP_AccurateMassSearch_3 -->
265 <test expect_num_outputs="3"> 271 <test expect_num_outputs="3">
266 <section name="adv_opts"> 272 <section name="adv_opts">
267 <param name="force" value="false"/> 273 <param name="force" value="false"/>
268 <param name="test" value="true"/> 274 <param name="test" value="true"/>
269 </section> 275 </section>
270 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> 276 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
271 <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 277 <output name="out" value="AccurateMassSearch_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
272 <param name="out_annotation_type" value="featureXML"/> 278 <param name="out_annotation_type" value="featureXML"/>
273 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 279 <output name="out_annotation" value="AccurateMassSearch_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
274 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> 280 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
275 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> 281 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
276 <section name="db"> 282 <section name="db">
277 <conditional name="mapping_cond"> 283 <conditional name="mapping_cond">
278 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> 284 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
297 <output name="ctd_out" ftype="xml"> 303 <output name="ctd_out" ftype="xml">
298 <assert_contents> 304 <assert_contents>
299 <is_valid_xml/> 305 <is_valid_xml/>
300 </assert_contents> 306 </assert_contents>
301 </output> 307 </output>
308 <assert_stdout>
309 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
310 </assert_stdout>
302 </test> 311 </test>
303 <!-- UTILS_AccurateMassSearch_5 --> 312 <!-- TOPP_AccurateMassSearch_5 -->
304 <test expect_num_outputs="3"> 313 <test expect_num_outputs="3">
305 <section name="adv_opts"> 314 <section name="adv_opts">
306 <param name="force" value="false"/> 315 <param name="force" value="false"/>
307 <param name="test" value="true"/> 316 <param name="test" value="true"/>
308 </section> 317 </section>
309 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> 318 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
310 <output name="out" file="AccurateMassSearch_5_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 319 <output name="out" value="AccurateMassSearch_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
311 <param name="out_annotation_type" value="oms"/> 320 <param name="out_annotation_type" value="oms"/>
312 <output name="out_annotation" file="AccurateMassSearch_5_output.tmp.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> 321 <output name="out_annotation" value="AccurateMassSearch_5_output.tmp.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
313 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> 322 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
314 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> 323 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
315 <section name="db"> 324 <section name="db">
316 <conditional name="mapping_cond"> 325 <conditional name="mapping_cond">
317 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> 326 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
336 <output name="ctd_out" ftype="xml"> 345 <output name="ctd_out" ftype="xml">
337 <assert_contents> 346 <assert_contents>
338 <is_valid_xml/> 347 <is_valid_xml/>
339 </assert_contents> 348 </assert_contents>
340 </output> 349 </output>
350 <assert_stdout>
351 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
352 </assert_stdout>
341 </test> 353 </test>
342 <!-- UTILS_AccurateMassSearch_6 --> 354 <!-- TOPP_AccurateMassSearch_6 -->
343 <test expect_num_outputs="3"> 355 <test expect_num_outputs="3">
344 <section name="adv_opts"> 356 <section name="adv_opts">
345 <param name="force" value="false"/> 357 <param name="force" value="false"/>
346 <param name="test" value="true"/> 358 <param name="test" value="true"/>
347 </section> 359 </section>
348 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> 360 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
349 <output name="out" file="AccurateMassSearch_6_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 361 <output name="out" value="AccurateMassSearch_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
350 <param name="out_annotation_type" value="featureXML"/> 362 <param name="out_annotation_type" value="featureXML"/>
351 <output name="out_annotation" file="AccurateMassSearch_6_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 363 <output name="out_annotation" value="AccurateMassSearch_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
352 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> 364 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
353 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> 365 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
354 <section name="db"> 366 <section name="db">
355 <conditional name="mapping_cond"> 367 <conditional name="mapping_cond">
356 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> 368 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
375 <output name="ctd_out" ftype="xml"> 387 <output name="ctd_out" ftype="xml">
376 <assert_contents> 388 <assert_contents>
377 <is_valid_xml/> 389 <is_valid_xml/>
378 </assert_contents> 390 </assert_contents>
379 </output> 391 </output>
392 <assert_stdout>
393 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
394 </assert_stdout>
380 </test> 395 </test>
381 </tests> 396 </tests>
382 <help><![CDATA[Match MS signals to molecules from a database by mass. 397 <help><![CDATA[Match MS signals to molecules from a database by mass.
383 398
384 399
385 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AccurateMassSearch.html]]></help> 400 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_AccurateMassSearch.html]]></help>
386 <expand macro="references"/> 401 <expand macro="references"/>
387 </tool> 402 </tool>