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comparison AccurateMassSearch.xml @ 16:532cf3ddcc91 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:05:06 +0000
parents 2dea459da18e
children 31e674c86840
comparison
equal deleted inserted replaced
15:a12a392cc85f 16:532cf3ddcc91
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Match MS signals to molecules from a database by mass.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">AccurateMassSearch</token> 7 <token name="@EXECUTABLE@">AccurateMassSearch</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
28 #end if 26 #end if
29 #if $negative_adducts: 27 #if $negative_adducts:
30 mkdir negative_adducts && 28 mkdir negative_adducts &&
31 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' && 29 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
32 #end if 30 #end if
33 #if $db.mapping: 31 #if $db.mapping_cond.mapping:
34 mkdir db.mapping && 32 mkdir db.mapping_cond.mapping &&
35 ${ ' '.join(["ln -s '%s' 'db.mapping/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _]) } 33 #if $db.mapping_cond.mapping_select == "no"
36 #end if 34 mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} &&
37 #if $db.struct: 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])}
38 mkdir db.struct && 36 #else
39 ${ ' '.join(["ln -s '%s' 'db.struct/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _]) } 37 ln -s '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' &&
38 #end if
39 #end if
40 #if $db.struct_cond.struct:
41 mkdir db.struct_cond.struct &&
42 #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])} &&
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])}
45 #else
46 ln -s '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' &&
47 #end if
40 #end if 48 #end if
41 49
42 ## Main program call 50 ## Main program call
43 51
44 set -o pipefail && 52 set -o pipefail &&
49 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 57 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
50 -out 58 -out
51 'out/output.${gxy2omsext("mztab")}' 59 'out/output.${gxy2omsext("mztab")}'
52 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 60 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
53 -out_annotation 61 -out_annotation
54 'out_annotation/output.${in.ext}' 62 'out_annotation/output.${out_annotation_type}'
55 #end if 63 #end if
56 #if $positive_adducts: 64 #if $positive_adducts:
57 -positive_adducts 65 -positive_adducts
58 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' 66 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)'
59 #end if 67 #end if
60 #if $negative_adducts: 68 #if $negative_adducts:
61 -negative_adducts 69 -negative_adducts
62 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' 70 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)'
63 #end if 71 #end if
64 #if $db.mapping: 72 #if $db.mapping_cond.mapping:
65 -db:mapping 73 -db:mapping
66 ${' '.join(["'db.mapping/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])} 74 #if $db.mapping_cond.mapping_select == "no"
67 #end if 75 ${' '.join(["'db.mapping_cond.mapping/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
68 #if $db.struct: 76 #else
77 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)'
78 #end if
79 #end if
80 #if $db.struct_cond.struct:
69 -db:struct 81 -db:struct
70 ${' '.join(["'db.struct/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])} 82 #if $db.struct_cond.struct_select == "no"
83 ${' '.join(["'db.struct_cond.struct/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
84 #else
85 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)'
86 #end if
71 #end if 87 #end if
72 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 88 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
73 | tee '$stdout' 89 | tee '$stdout'
74 #end if 90 #end if
75 91
76 ## Postprocessing 92 ## Postprocessing
77 && mv 'out/output.${gxy2omsext("mztab")}' '$out' 93 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
78 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 94 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
79 && mv 'out_annotation/output.${in.ext}' '$out_annotation' 95 && mv 'out_annotation/output.${out_annotation_type}' '$out_annotation'
80 #end if 96 #end if
81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 97 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
82 && mv '@EXECUTABLE@.ctd' '$ctd_out' 98 && mv '@EXECUTABLE@.ctd' '$ctd_out'
83 #end if]]></command> 99 #end if]]></command>
84 <configfiles> 100 <configfiles>
85 <inputs name="args_json" data_style="paths"/> 101 <inputs name="args_json" data_style="paths"/>
86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
87 </configfiles> 103 </configfiles>
88 <inputs> 104 <inputs>
89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/> 105 <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
90 <param name="positive_adducts" 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)"/> 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.)">
91 <param name="negative_adducts" argument="-negative_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential negative adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/> 107 <option value="featureXML">featurexml</option>
108 <option value="consensusXML">consensusxml</option>
109 <option value="oms">sqlite (oms)</option>
110 </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)"/>
112 <param argument="-negative_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential negative adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
92 <section name="db" title="Database files which contain the identifications" help="" expanded="false"> 113 <section name="db" title="Database files which contain the identifications" help="" expanded="false">
93 <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)"/> 114 <conditional name="mapping_cond">
94 <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)"/> 115 <param name="mapping_select" type="select" label="Run tool in batch mode for -mapping">
116 <option value="no">No: process all datasets jointly</option>
117 <option value="yes">Yes: process each dataset in an independent job</option>
118 </param>
119 <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)"/>
121 </when>
122 <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)"/>
124 </when>
125 </conditional>
126 <conditional name="struct_cond">
127 <param name="struct_select" type="select" label="Run tool in batch mode for -struct">
128 <option value="no">No: process all datasets jointly</option>
129 <option value="yes">Yes: process each dataset in an independent job</option>
130 </param>
131 <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)"/>
133 </when>
134 <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)"/>
136 </when>
137 </conditional>
95 </section> 138 </section>
96 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 139 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
97 <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=""/> 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=""/>
98 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" 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="">
99 <option value="ppm" selected="true">ppm</option> 142 <option value="ppm" selected="true">ppm</option>
100 <option value="Da">Da</option> 143 <option value="Da">Da</option>
101 <expand macro="list_string_san"/> 144 <expand macro="list_string_san" name="mass_error_unit"/>
102 </param> 145 </param>
103 <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" 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"> 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">
104 <option value="positive" selected="true">positive</option> 147 <option value="positive" selected="true">positive</option>
105 <option value="negative">negative</option> 148 <option value="negative">negative</option>
106 <option value="auto">auto</option> 149 <option value="auto">auto</option>
107 <expand macro="list_string_san"/> 150 <expand macro="list_string_san" name="ionization_mode"/>
108 </param> 151 </param>
109 <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=""/> 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=""/>
110 <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=""/> 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=""/>
111 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep features that did not yield any DB hit" 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=""/>
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="">
156 <option value="legacy" selected="true">legacy</option>
157 <option value="ID">ID</option>
158 <expand macro="list_string_san" name="id_format"/>
159 </param>
112 <section name="mzTab" title="" help="" expanded="false"> 160 <section name="mzTab" title="" help="" expanded="false">
113 <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=""/> 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=""/>
114 </section> 162 </section>
115 </section> 163 </section>
116 <expand macro="adv_opts_macro"> 164 <expand macro="adv_opts_macro">
117 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 165 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
118 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 166 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
119 <expand macro="list_string_san"/> 167 <expand macro="list_string_san" name="test"/>
120 </param> 168 </param>
121 </expand> 169 </expand>
122 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 170 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
123 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option> 171 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option>
124 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 172 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
125 </param> 173 </param>
126 </inputs> 174 </inputs>
127 <outputs> 175 <outputs>
128 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 176 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
129 <data name="out_annotation" label="${tool.name} on ${on_string}: out_annotation" format_source="in" metadata_source="in"> 177 <data name="out_annotation" label="${tool.name} on ${on_string}: out_annotation" format="consensusxml">
178 <change_format>
179 <when input="out_annotation_type" value="featureXML" format="featurexml"/>
180 <when input="out_annotation_type" value="oms" format="sqlite"/>
181 </change_format>
130 <filter>OPTIONAL_OUTPUTS is not None and "out_annotation_FLAG" in OPTIONAL_OUTPUTS</filter> 182 <filter>OPTIONAL_OUTPUTS is not None and "out_annotation_FLAG" in OPTIONAL_OUTPUTS</filter>
131 </data> 183 </data>
132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 184 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 185 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
134 </data> 186 </data>
135 </outputs> 187 </outputs>
136 <tests> 188 <tests><!-- UTILS_AccurateMassSearch_1 -->
137 <expand macro="autotest_AccurateMassSearch"/> 189 <test expect_num_outputs="2">
138 <expand macro="manutest_AccurateMassSearch"/> 190 <section name="adv_opts">
191 <param name="force" value="false"/>
192 <param name="test" value="true"/>
193 </section>
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"/>
196 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
197 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
198 <section name="db">
199 <conditional name="mapping_cond">
200 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
201 </conditional>
202 <conditional name="struct_cond">
203 <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
204 </conditional>
205 </section>
206 <section name="algorithm">
207 <param name="mass_error_value" value="5.0"/>
208 <param name="mass_error_unit" value="ppm"/>
209 <param name="ionization_mode" value="positive"/>
210 <param name="isotopic_similarity" value="false"/>
211 <param name="use_feature_adducts" value="false"/>
212 <param name="keep_unidentified_masses" value="true"/>
213 <param name="id_format" value="legacy"/>
214 <section name="mzTab">
215 <param name="exportIsotopeIntensities" value="false"/>
216 </section>
217 </section>
218 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
219 <output name="ctd_out" ftype="xml">
220 <assert_contents>
221 <is_valid_xml/>
222 </assert_contents>
223 </output>
224 </test>
225 <!-- UTILS_AccurateMassSearch_2 -->
226 <test expect_num_outputs="3">
227 <section name="adv_opts">
228 <param name="force" value="false"/>
229 <param name="test" value="true"/>
230 </section>
231 <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"/>
233 <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"/>
235 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
236 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
237 <section name="db">
238 <conditional name="mapping_cond">
239 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
240 </conditional>
241 <conditional name="struct_cond">
242 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
243 </conditional>
244 </section>
245 <section name="algorithm">
246 <param name="mass_error_value" value="5.0"/>
247 <param name="mass_error_unit" value="ppm"/>
248 <param name="ionization_mode" value="positive"/>
249 <param name="isotopic_similarity" value="false"/>
250 <param name="use_feature_adducts" value="false"/>
251 <param name="keep_unidentified_masses" value="false"/>
252 <param name="id_format" value="legacy"/>
253 <section name="mzTab">
254 <param name="exportIsotopeIntensities" value="true"/>
255 </section>
256 </section>
257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
258 <output name="ctd_out" ftype="xml">
259 <assert_contents>
260 <is_valid_xml/>
261 </assert_contents>
262 </output>
263 </test>
264 <!-- UTILS_AccurateMassSearch_3 -->
265 <test expect_num_outputs="3">
266 <section name="adv_opts">
267 <param name="force" value="false"/>
268 <param name="test" value="true"/>
269 </section>
270 <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"/>
272 <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"/>
274 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
275 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
276 <section name="db">
277 <conditional name="mapping_cond">
278 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
279 </conditional>
280 <conditional name="struct_cond">
281 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
282 </conditional>
283 </section>
284 <section name="algorithm">
285 <param name="mass_error_value" value="5.0"/>
286 <param name="mass_error_unit" value="ppm"/>
287 <param name="ionization_mode" value="positive"/>
288 <param name="isotopic_similarity" value="false"/>
289 <param name="use_feature_adducts" value="false"/>
290 <param name="keep_unidentified_masses" value="true"/>
291 <param name="id_format" value="legacy"/>
292 <section name="mzTab">
293 <param name="exportIsotopeIntensities" value="false"/>
294 </section>
295 </section>
296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
297 <output name="ctd_out" ftype="xml">
298 <assert_contents>
299 <is_valid_xml/>
300 </assert_contents>
301 </output>
302 </test>
303 <!-- UTILS_AccurateMassSearch_5 -->
304 <test expect_num_outputs="3">
305 <section name="adv_opts">
306 <param name="force" value="false"/>
307 <param name="test" value="true"/>
308 </section>
309 <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"/>
311 <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"/>
313 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
314 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
315 <section name="db">
316 <conditional name="mapping_cond">
317 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
318 </conditional>
319 <conditional name="struct_cond">
320 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
321 </conditional>
322 </section>
323 <section name="algorithm">
324 <param name="mass_error_value" value="5.0"/>
325 <param name="mass_error_unit" value="ppm"/>
326 <param name="ionization_mode" value="positive"/>
327 <param name="isotopic_similarity" value="false"/>
328 <param name="use_feature_adducts" value="false"/>
329 <param name="keep_unidentified_masses" value="true"/>
330 <param name="id_format" value="ID"/>
331 <section name="mzTab">
332 <param name="exportIsotopeIntensities" value="false"/>
333 </section>
334 </section>
335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
336 <output name="ctd_out" ftype="xml">
337 <assert_contents>
338 <is_valid_xml/>
339 </assert_contents>
340 </output>
341 </test>
342 <!-- UTILS_AccurateMassSearch_6 -->
343 <test expect_num_outputs="3">
344 <section name="adv_opts">
345 <param name="force" value="false"/>
346 <param name="test" value="true"/>
347 </section>
348 <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"/>
350 <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"/>
352 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
353 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
354 <section name="db">
355 <conditional name="mapping_cond">
356 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
357 </conditional>
358 <conditional name="struct_cond">
359 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
360 </conditional>
361 </section>
362 <section name="algorithm">
363 <param name="mass_error_value" value="5.0"/>
364 <param name="mass_error_unit" value="ppm"/>
365 <param name="ionization_mode" value="positive"/>
366 <param name="isotopic_similarity" value="false"/>
367 <param name="use_feature_adducts" value="false"/>
368 <param name="keep_unidentified_masses" value="true"/>
369 <param name="id_format" value="ID"/>
370 <section name="mzTab">
371 <param name="exportIsotopeIntensities" value="false"/>
372 </section>
373 </section>
374 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
375 <output name="ctd_out" ftype="xml">
376 <assert_contents>
377 <is_valid_xml/>
378 </assert_contents>
379 </output>
380 </test>
139 </tests> 381 </tests>
140 <help><![CDATA[Match MS signals to molecules from a database by mass. 382 <help><![CDATA[Match MS signals to molecules from a database by mass.
141 383
142 384
143 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_AccurateMassSearch.html]]></help> 385 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AccurateMassSearch.html]]></help>
144 <expand macro="references"/> 386 <expand macro="references"/>
145 </tool> 387 </tool>