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comparison TargetedFileConverter.xml @ 12:43b9ed22e8ce draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:37:15 +0000
parents 9c70a651a53e
children
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11:9c70a651a53e 12:43b9ed22e8ce
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: [Targeted Experiments]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description> 4 <description>Converts different transition files for targeted proteomics / metabolomics analysis</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">TargetedFileConverter</token> 6 <token name="@EXECUTABLE@">TargetedFileConverter</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 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> 41 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/TOPP_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>
43 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense"> 42 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
44 <option value="TraML">traml</option> 43 <option value="TraML">traml</option>
45 <option value="pqp">pqp</option> 44 <option value="pqp">pqp</option>
46 <option value="tsv">tabular (tsv)</option> 45 <option value="tsv">tabular (tsv)</option>
46 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
47 <expand macro="list_string_san" name="out_type"/> 47 <expand macro="list_string_san" name="out_type"/>
48 </param> 48 </param>
49 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 49 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
50 <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="true" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help=""> 50 <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
51 <option value="iRT" selected="true">iRT</option> 51 <option value="iRT" selected="true">iRT</option>
52 <option value="seconds">seconds</option> 52 <option value="seconds">seconds</option>
53 <option value="minutes">minutes</option> 53 <option value="minutes">minutes</option>
54 <expand macro="list_string_san" name="retentionTimeInterpretation"/> 54 <expand macro="list_string_san" name="retentionTimeInterpretation"/>
55 </param> 55 </param>
57 <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/> 57 <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
58 </section> 58 </section>
59 <expand macro="adv_opts_macro"> 59 <expand macro="adv_opts_macro">
60 <param argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/> 60 <param argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/>
61 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 61 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
62 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 62 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
63 <expand macro="list_string_san" name="test"/> 63 <expand macro="list_string_san" name="test"/>
64 </param> 64 </param>
65 </expand> 65 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
76 </data> 76 </data>
77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
79 </data> 79 </data>
80 </outputs> 80 </outputs>
81 <tests><!-- TOPP_ConvertTSVToTraML_test_1 --> 81 <tests>
82 <!-- TOPP_ConvertTSVToTraML_test_1 -->
82 <test expect_num_outputs="2"> 83 <test expect_num_outputs="2">
83 <section name="adv_opts"> 84 <section name="adv_opts">
84 <param name="legacy_traml_id" value="false"/> 85 <param name="legacy_traml_id" value="false"/>
85 <param name="force" value="false"/> 86 <param name="force" value="false"/>
86 <param name="test" value="true"/> 87 <param name="test" value="true"/>
87 </section> 88 </section>
88 <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> 89 <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
89 <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 90 <output name="out" value="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
90 <param name="out_type" value="TraML"/> 91 <param name="out_type" value="TraML"/>
91 <section name="algorithm"> 92 <section name="algorithm">
92 <param name="retentionTimeInterpretation" value="iRT"/> 93 <param name="retentionTimeInterpretation" value="iRT"/>
93 <param name="override_group_label_check" value="false"/> 94 <param name="override_group_label_check" value="false"/>
94 <param name="force_invalid_mods" value="false"/> 95 <param name="force_invalid_mods" value="false"/>
95 </section> 96 </section>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 97 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml"> 98 <output name="ctd_out" ftype="xml">
98 <assert_contents> 99 <assert_contents>
99 <is_valid_xml/> 100 <is_valid_xml/>
100 </assert_contents> 101 </assert_contents>
101 </output> 102 </output>
103 <assert_stdout>
104 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
105 </assert_stdout>
102 </test> 106 </test>
103 <!-- TOPP_ConvertTSVToTraML_test_2 --> 107 <!-- TOPP_ConvertTSVToTraML_test_2 -->
104 <test expect_num_outputs="2"> 108 <test expect_num_outputs="2">
105 <section name="adv_opts"> 109 <section name="adv_opts">
106 <param name="legacy_traml_id" value="false"/> 110 <param name="legacy_traml_id" value="false"/>
107 <param name="force" value="false"/> 111 <param name="force" value="false"/>
108 <param name="test" value="true"/> 112 <param name="test" value="true"/>
109 </section> 113 </section>
110 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> 114 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
111 <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 115 <output name="out" value="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
112 <param name="out_type" value="TraML"/> 116 <param name="out_type" value="TraML"/>
113 <section name="algorithm"> 117 <section name="algorithm">
114 <param name="retentionTimeInterpretation" value="minutes"/> 118 <param name="retentionTimeInterpretation" value="minutes"/>
115 <param name="override_group_label_check" value="false"/> 119 <param name="override_group_label_check" value="false"/>
116 <param name="force_invalid_mods" value="false"/> 120 <param name="force_invalid_mods" value="false"/>
119 <output name="ctd_out" ftype="xml"> 123 <output name="ctd_out" ftype="xml">
120 <assert_contents> 124 <assert_contents>
121 <is_valid_xml/> 125 <is_valid_xml/>
122 </assert_contents> 126 </assert_contents>
123 </output> 127 </output>
128 <assert_stdout>
129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
130 </assert_stdout>
124 </test> 131 </test>
125 <!-- TOPP_ConvertTSVToTraML_test_3 --> 132 <!-- TOPP_ConvertTSVToTraML_test_3 -->
126 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
127 <section name="adv_opts"> 134 <section name="adv_opts">
128 <param name="legacy_traml_id" value="false"/> 135 <param name="legacy_traml_id" value="false"/>
129 <param name="force" value="false"/> 136 <param name="force" value="false"/>
130 <param name="test" value="true"/> 137 <param name="test" value="true"/>
131 </section> 138 </section>
132 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> 139 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
133 <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 140 <output name="out" value="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
134 <param name="out_type" value="TraML"/> 141 <param name="out_type" value="TraML"/>
135 <section name="algorithm"> 142 <section name="algorithm">
136 <param name="retentionTimeInterpretation" value="seconds"/> 143 <param name="retentionTimeInterpretation" value="seconds"/>
137 <param name="override_group_label_check" value="false"/> 144 <param name="override_group_label_check" value="false"/>
138 <param name="force_invalid_mods" value="false"/> 145 <param name="force_invalid_mods" value="false"/>
141 <output name="ctd_out" ftype="xml"> 148 <output name="ctd_out" ftype="xml">
142 <assert_contents> 149 <assert_contents>
143 <is_valid_xml/> 150 <is_valid_xml/>
144 </assert_contents> 151 </assert_contents>
145 </output> 152 </output>
153 <assert_stdout>
154 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
155 </assert_stdout>
146 </test> 156 </test>
147 <!-- TOPP_ConvertTSVToTraML_test_4 --> 157 <!-- TOPP_ConvertTSVToTraML_test_4 -->
148 <test expect_num_outputs="2"> 158 <test expect_num_outputs="2">
149 <section name="adv_opts"> 159 <section name="adv_opts">
150 <param name="legacy_traml_id" value="false"/> 160 <param name="legacy_traml_id" value="false"/>
151 <param name="force" value="false"/> 161 <param name="force" value="false"/>
152 <param name="test" value="true"/> 162 <param name="test" value="true"/>
153 </section> 163 </section>
154 <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> 164 <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
155 <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 165 <output name="out" value="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
156 <param name="out_type" value="TraML"/> 166 <param name="out_type" value="TraML"/>
157 <section name="algorithm"> 167 <section name="algorithm">
158 <param name="retentionTimeInterpretation" value="iRT"/> 168 <param name="retentionTimeInterpretation" value="iRT"/>
159 <param name="override_group_label_check" value="false"/> 169 <param name="override_group_label_check" value="false"/>
160 <param name="force_invalid_mods" value="false"/> 170 <param name="force_invalid_mods" value="false"/>
161 </section> 171 </section>
162 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
163 <output name="ctd_out" ftype="xml"> 173 <output name="ctd_out" ftype="xml">
164 <assert_contents> 174 <assert_contents>
165 <is_valid_xml/> 175 <is_valid_xml/>
166 </assert_contents> 176 </assert_contents>
167 </output> 177 </output>
178 <assert_stdout>
179 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
180 </assert_stdout>
168 </test> 181 </test>
169 <!-- TOPP_ConvertTSVToTraML_test_5 --> 182 <!-- TOPP_ConvertTSVToTraML_test_5 -->
170 <test expect_num_outputs="2"> 183 <test expect_num_outputs="2">
171 <section name="adv_opts"> 184 <section name="adv_opts">
172 <param name="legacy_traml_id" value="false"/> 185 <param name="legacy_traml_id" value="false"/>
173 <param name="force" value="false"/> 186 <param name="force" value="false"/>
174 <param name="test" value="true"/> 187 <param name="test" value="true"/>
175 </section> 188 </section>
176 <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> 189 <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
177 <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 190 <output name="out" value="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
178 <param name="out_type" value="TraML"/> 191 <param name="out_type" value="TraML"/>
179 <section name="algorithm"> 192 <section name="algorithm">
180 <param name="retentionTimeInterpretation" value="iRT"/> 193 <param name="retentionTimeInterpretation" value="iRT"/>
181 <param name="override_group_label_check" value="false"/> 194 <param name="override_group_label_check" value="false"/>
182 <param name="force_invalid_mods" value="false"/> 195 <param name="force_invalid_mods" value="false"/>
183 </section> 196 </section>
184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
185 <output name="ctd_out" ftype="xml"> 198 <output name="ctd_out" ftype="xml">
186 <assert_contents> 199 <assert_contents>
187 <is_valid_xml/> 200 <is_valid_xml/>
188 </assert_contents> 201 </assert_contents>
189 </output> 202 </output>
203 <assert_stdout>
204 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
205 </assert_stdout>
190 </test> 206 </test>
191 <!-- TOPP_ConvertTSVToTraML_test_6 --> 207 <!-- TOPP_ConvertTSVToTraML_test_6 -->
192 <test expect_num_outputs="2"> 208 <test expect_num_outputs="2">
193 <section name="adv_opts"> 209 <section name="adv_opts">
194 <param name="legacy_traml_id" value="false"/> 210 <param name="legacy_traml_id" value="false"/>
195 <param name="force" value="false"/> 211 <param name="force" value="false"/>
196 <param name="test" value="true"/> 212 <param name="test" value="true"/>
197 </section> 213 </section>
198 <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> 214 <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
199 <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 215 <output name="out" value="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
200 <param name="out_type" value="TraML"/> 216 <param name="out_type" value="TraML"/>
201 <section name="algorithm"> 217 <section name="algorithm">
202 <param name="retentionTimeInterpretation" value="iRT"/> 218 <param name="retentionTimeInterpretation" value="iRT"/>
203 <param name="override_group_label_check" value="false"/> 219 <param name="override_group_label_check" value="false"/>
204 <param name="force_invalid_mods" value="false"/> 220 <param name="force_invalid_mods" value="false"/>
205 </section> 221 </section>
206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 222 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
207 <output name="ctd_out" ftype="xml"> 223 <output name="ctd_out" ftype="xml">
208 <assert_contents> 224 <assert_contents>
209 <is_valid_xml/> 225 <is_valid_xml/>
210 </assert_contents> 226 </assert_contents>
211 </output> 227 </output>
228 <assert_stdout>
229 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
230 </assert_stdout>
212 </test> 231 </test>
213 <!-- TOPP_ConvertTSVToTraML_test_7 --> 232 <!-- TOPP_ConvertTSVToTraML_test_7 -->
214 <test expect_num_outputs="2"> 233 <test expect_num_outputs="2">
215 <section name="adv_opts"> 234 <section name="adv_opts">
216 <param name="legacy_traml_id" value="false"/> 235 <param name="legacy_traml_id" value="false"/>
217 <param name="force" value="false"/> 236 <param name="force" value="false"/>
218 <param name="test" value="true"/> 237 <param name="test" value="true"/>
219 </section> 238 </section>
220 <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> 239 <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
221 <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 240 <output name="out" value="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
222 <param name="out_type" value="TraML"/> 241 <param name="out_type" value="TraML"/>
223 <section name="algorithm"> 242 <section name="algorithm">
224 <param name="retentionTimeInterpretation" value="iRT"/> 243 <param name="retentionTimeInterpretation" value="iRT"/>
225 <param name="override_group_label_check" value="false"/> 244 <param name="override_group_label_check" value="false"/>
226 <param name="force_invalid_mods" value="false"/> 245 <param name="force_invalid_mods" value="false"/>
227 </section> 246 </section>
228 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
229 <output name="ctd_out" ftype="xml"> 248 <output name="ctd_out" ftype="xml">
230 <assert_contents> 249 <assert_contents>
231 <is_valid_xml/> 250 <is_valid_xml/>
232 </assert_contents> 251 </assert_contents>
233 </output> 252 </output>
253 <assert_stdout>
254 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
255 </assert_stdout>
256 </test>
257 <!-- TOPP_TargetedFileConverter_test_1_prepare -->
258 <test expect_num_outputs="2">
259 <section name="adv_opts">
260 <param name="legacy_traml_id" value="false"/>
261 <param name="force" value="false"/>
262 <param name="test" value="true"/>
263 </section>
264 <param name="in" value="TargetedFileConverter_1_input.TraML"/>
265 <output name="out" value="TargetedFileConverter_1_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
266 <param name="out_type" value="pqp"/>
267 <section name="algorithm">
268 <param name="retentionTimeInterpretation" value="iRT"/>
269 <param name="override_group_label_check" value="false"/>
270 <param name="force_invalid_mods" value="false"/>
271 </section>
272 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
273 <output name="ctd_out" ftype="xml">
274 <assert_contents>
275 <is_valid_xml/>
276 </assert_contents>
277 </output>
278 <assert_stdout>
279 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
280 </assert_stdout>
234 </test> 281 </test>
235 <!-- TOPP_TargetedFileConverter_test_1 --> 282 <!-- TOPP_TargetedFileConverter_test_1 -->
236 <test expect_num_outputs="2"> 283 <test expect_num_outputs="2">
237 <section name="adv_opts"> 284 <section name="adv_opts">
238 <param name="legacy_traml_id" value="false"/> 285 <param name="legacy_traml_id" value="false"/>
239 <param name="force" value="false"/> 286 <param name="force" value="false"/>
240 <param name="test" value="true"/> 287 <param name="test" value="true"/>
241 </section> 288 </section>
242 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> 289 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
243 <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 290 <output name="out" value="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
244 <param name="out_type" value="TraML"/> 291 <param name="out_type" value="TraML"/>
245 <section name="algorithm"> 292 <section name="algorithm">
246 <param name="retentionTimeInterpretation" value="iRT"/> 293 <param name="retentionTimeInterpretation" value="iRT"/>
247 <param name="override_group_label_check" value="false"/> 294 <param name="override_group_label_check" value="false"/>
248 <param name="force_invalid_mods" value="false"/> 295 <param name="force_invalid_mods" value="false"/>
249 </section> 296 </section>
250 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 297 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
251 <output name="ctd_out" ftype="xml"> 298 <output name="ctd_out" ftype="xml">
252 <assert_contents> 299 <assert_contents>
253 <is_valid_xml/> 300 <is_valid_xml/>
254 </assert_contents> 301 </assert_contents>
255 </output> 302 </output>
303 <assert_stdout>
304 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
305 </assert_stdout>
256 </test> 306 </test>
257 <!-- TOPP_TargetedFileConverter_test_2 --> 307 <!-- TOPP_TargetedFileConverter_test_2 -->
258 <test expect_num_outputs="2"> 308 <test expect_num_outputs="2">
259 <section name="adv_opts"> 309 <section name="adv_opts">
260 <param name="legacy_traml_id" value="true"/> 310 <param name="legacy_traml_id" value="true"/>
261 <param name="force" value="false"/> 311 <param name="force" value="false"/>
262 <param name="test" value="true"/> 312 <param name="test" value="true"/>
263 </section> 313 </section>
264 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> 314 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
265 <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 315 <output name="out" value="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
266 <param name="out_type" value="TraML"/> 316 <param name="out_type" value="TraML"/>
267 <section name="algorithm"> 317 <section name="algorithm">
268 <param name="retentionTimeInterpretation" value="iRT"/> 318 <param name="retentionTimeInterpretation" value="iRT"/>
269 <param name="override_group_label_check" value="false"/> 319 <param name="override_group_label_check" value="false"/>
270 <param name="force_invalid_mods" value="false"/> 320 <param name="force_invalid_mods" value="false"/>
271 </section> 321 </section>
272 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 322 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
273 <output name="ctd_out" ftype="xml"> 323 <output name="ctd_out" ftype="xml">
274 <assert_contents> 324 <assert_contents>
275 <is_valid_xml/> 325 <is_valid_xml/>
276 </assert_contents> 326 </assert_contents>
277 </output> 327 </output>
328 <assert_stdout>
329 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
330 </assert_stdout>
331 </test>
332 <!-- TOPP_TargetedFileConverter_test_3_prepare -->
333 <test expect_num_outputs="2">
334 <section name="adv_opts">
335 <param name="legacy_traml_id" value="false"/>
336 <param name="force" value="false"/>
337 <param name="test" value="true"/>
338 </section>
339 <param name="in" value="TargetedFileConverter_3_input.TraML"/>
340 <output name="out" value="TargetedFileConverter_3_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
341 <param name="out_type" value="pqp"/>
342 <section name="algorithm">
343 <param name="retentionTimeInterpretation" value="iRT"/>
344 <param name="override_group_label_check" value="false"/>
345 <param name="force_invalid_mods" value="false"/>
346 </section>
347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
348 <output name="ctd_out" ftype="xml">
349 <assert_contents>
350 <is_valid_xml/>
351 </assert_contents>
352 </output>
353 <assert_stdout>
354 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
355 </assert_stdout>
278 </test> 356 </test>
279 <!-- TOPP_TargetedFileConverter_test_3 --> 357 <!-- TOPP_TargetedFileConverter_test_3 -->
280 <test expect_num_outputs="2"> 358 <test expect_num_outputs="2">
281 <section name="adv_opts"> 359 <section name="adv_opts">
282 <param name="legacy_traml_id" value="false"/> 360 <param name="legacy_traml_id" value="false"/>
283 <param name="force" value="false"/> 361 <param name="force" value="false"/>
284 <param name="test" value="true"/> 362 <param name="test" value="true"/>
285 </section> 363 </section>
286 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> 364 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
287 <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 365 <output name="out" value="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
288 <param name="out_type" value="TraML"/> 366 <param name="out_type" value="TraML"/>
289 <section name="algorithm"> 367 <section name="algorithm">
290 <param name="retentionTimeInterpretation" value="iRT"/> 368 <param name="retentionTimeInterpretation" value="iRT"/>
291 <param name="override_group_label_check" value="false"/> 369 <param name="override_group_label_check" value="false"/>
292 <param name="force_invalid_mods" value="false"/> 370 <param name="force_invalid_mods" value="false"/>
293 </section> 371 </section>
294 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 372 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
295 <output name="ctd_out" ftype="xml"> 373 <output name="ctd_out" ftype="xml">
296 <assert_contents> 374 <assert_contents>
297 <is_valid_xml/> 375 <is_valid_xml/>
298 </assert_contents> 376 </assert_contents>
299 </output> 377 </output>
378 <assert_stdout>
379 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
380 </assert_stdout>
300 </test> 381 </test>
301 <!-- TOPP_TargetedFileConverter_test_4 --> 382 <!-- TOPP_TargetedFileConverter_test_4 -->
302 <test expect_num_outputs="2"> 383 <test expect_num_outputs="2">
303 <section name="adv_opts"> 384 <section name="adv_opts">
304 <param name="legacy_traml_id" value="true"/> 385 <param name="legacy_traml_id" value="true"/>
305 <param name="force" value="false"/> 386 <param name="force" value="false"/>
306 <param name="test" value="true"/> 387 <param name="test" value="true"/>
307 </section> 388 </section>
308 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> 389 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
309 <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 390 <output name="out" value="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
310 <param name="out_type" value="TraML"/> 391 <param name="out_type" value="TraML"/>
311 <section name="algorithm"> 392 <section name="algorithm">
312 <param name="retentionTimeInterpretation" value="iRT"/> 393 <param name="retentionTimeInterpretation" value="iRT"/>
313 <param name="override_group_label_check" value="false"/> 394 <param name="override_group_label_check" value="false"/>
314 <param name="force_invalid_mods" value="false"/> 395 <param name="force_invalid_mods" value="false"/>
315 </section> 396 </section>
316 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 397 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
317 <output name="ctd_out" ftype="xml"> 398 <output name="ctd_out" ftype="xml">
318 <assert_contents> 399 <assert_contents>
319 <is_valid_xml/> 400 <is_valid_xml/>
320 </assert_contents> 401 </assert_contents>
321 </output> 402 </output>
403 <assert_stdout>
404 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
405 </assert_stdout>
406 </test>
407 <!-- TOPP_TargetedFileConverter_test_10_prepare -->
408 <test expect_num_outputs="2">
409 <section name="adv_opts">
410 <param name="legacy_traml_id" value="true"/>
411 <param name="force" value="false"/>
412 <param name="test" value="true"/>
413 </section>
414 <param name="in" value="TargetedFileConverter_10_input.pqp"/>
415 <output name="out" value="TargetedFileConverter_10_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/>
416 <param name="out_type" value="TraML"/>
417 <section name="algorithm">
418 <param name="retentionTimeInterpretation" value="iRT"/>
419 <param name="override_group_label_check" value="false"/>
420 <param name="force_invalid_mods" value="false"/>
421 </section>
422 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
423 <output name="ctd_out" ftype="xml">
424 <assert_contents>
425 <is_valid_xml/>
426 </assert_contents>
427 </output>
428 <assert_stdout>
429 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
430 </assert_stdout>
322 </test> 431 </test>
323 <!-- TOPP_TargetedFileConverter_test_10 --> 432 <!-- TOPP_TargetedFileConverter_test_10 -->
324 <test expect_num_outputs="2"> 433 <test expect_num_outputs="2">
325 <section name="adv_opts"> 434 <section name="adv_opts">
326 <param name="legacy_traml_id" value="false"/> 435 <param name="legacy_traml_id" value="false"/>
327 <param name="force" value="false"/> 436 <param name="force" value="false"/>
328 <param name="test" value="true"/> 437 <param name="test" value="true"/>
329 </section> 438 </section>
330 <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> 439 <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
331 <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 440 <output name="out" value="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
332 <param name="out_type" value="tsv"/> 441 <param name="out_type" value="tsv"/>
333 <section name="algorithm"> 442 <section name="algorithm">
334 <param name="retentionTimeInterpretation" value="iRT"/> 443 <param name="retentionTimeInterpretation" value="iRT"/>
335 <param name="override_group_label_check" value="false"/> 444 <param name="override_group_label_check" value="false"/>
336 <param name="force_invalid_mods" value="false"/> 445 <param name="force_invalid_mods" value="false"/>
339 <output name="ctd_out" ftype="xml"> 448 <output name="ctd_out" ftype="xml">
340 <assert_contents> 449 <assert_contents>
341 <is_valid_xml/> 450 <is_valid_xml/>
342 </assert_contents> 451 </assert_contents>
343 </output> 452 </output>
453 <assert_stdout>
454 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
455 </assert_stdout>
456 </test>
457 <!-- TOPP_TargetedFileConverter_test_11_prepare -->
458 <test expect_num_outputs="2">
459 <section name="adv_opts">
460 <param name="legacy_traml_id" value="false"/>
461 <param name="force" value="false"/>
462 <param name="test" value="true"/>
463 </section>
464 <param name="in" value="TargetedFileConverter_11_input.TraML"/>
465 <output name="out" value="TargetedFileConverter_11_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
466 <param name="out_type" value="pqp"/>
467 <section name="algorithm">
468 <param name="retentionTimeInterpretation" value="iRT"/>
469 <param name="override_group_label_check" value="false"/>
470 <param name="force_invalid_mods" value="false"/>
471 </section>
472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
473 <output name="ctd_out" ftype="xml">
474 <assert_contents>
475 <is_valid_xml/>
476 </assert_contents>
477 </output>
478 <assert_stdout>
479 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
480 </assert_stdout>
344 </test> 481 </test>
345 <!-- TOPP_TargetedFileConverter_test_11 --> 482 <!-- TOPP_TargetedFileConverter_test_11 -->
346 <test expect_num_outputs="2"> 483 <test expect_num_outputs="2">
347 <section name="adv_opts"> 484 <section name="adv_opts">
348 <param name="legacy_traml_id" value="false"/> 485 <param name="legacy_traml_id" value="false"/>
349 <param name="force" value="false"/> 486 <param name="force" value="false"/>
350 <param name="test" value="true"/> 487 <param name="test" value="true"/>
351 </section> 488 </section>
352 <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> 489 <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
353 <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 490 <output name="out" value="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
354 <param name="out_type" value="TraML"/> 491 <param name="out_type" value="TraML"/>
355 <section name="algorithm"> 492 <section name="algorithm">
356 <param name="retentionTimeInterpretation" value="iRT"/> 493 <param name="retentionTimeInterpretation" value="iRT"/>
357 <param name="override_group_label_check" value="false"/> 494 <param name="override_group_label_check" value="false"/>
358 <param name="force_invalid_mods" value="false"/> 495 <param name="force_invalid_mods" value="false"/>
359 </section> 496 </section>
360 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 497 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
361 <output name="ctd_out" ftype="xml"> 498 <output name="ctd_out" ftype="xml">
362 <assert_contents> 499 <assert_contents>
363 <is_valid_xml/> 500 <is_valid_xml/>
364 </assert_contents> 501 </assert_contents>
365 </output> 502 </output>
503 <assert_stdout>
504 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
505 </assert_stdout>
506 </test>
507 <!-- TOPP_TargetedFileConverter_test_8_prepare -->
508 <test expect_num_outputs="2">
509 <section name="adv_opts">
510 <param name="legacy_traml_id" value="false"/>
511 <param name="force" value="false"/>
512 <param name="test" value="true"/>
513 </section>
514 <param name="in" value="TargetedFileConverter_8_input.tsv" ftype="tabular"/>
515 <output name="out" value="TargetedFileConverter_8_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/>
516 <param name="out_type" value="TraML"/>
517 <section name="algorithm">
518 <param name="retentionTimeInterpretation" value="iRT"/>
519 <param name="override_group_label_check" value="true"/>
520 <param name="force_invalid_mods" value="false"/>
521 </section>
522 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
523 <output name="ctd_out" ftype="xml">
524 <assert_contents>
525 <is_valid_xml/>
526 </assert_contents>
527 </output>
528 <assert_stdout>
529 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
530 </assert_stdout>
366 </test> 531 </test>
367 <!-- TOPP_TargetedFileConverter_test_8 --> 532 <!-- TOPP_TargetedFileConverter_test_8 -->
368 <test expect_num_outputs="2"> 533 <test expect_num_outputs="2">
369 <section name="adv_opts"> 534 <section name="adv_opts">
370 <param name="legacy_traml_id" value="false"/> 535 <param name="legacy_traml_id" value="false"/>
371 <param name="force" value="false"/> 536 <param name="force" value="false"/>
372 <param name="test" value="true"/> 537 <param name="test" value="true"/>
373 </section> 538 </section>
374 <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> 539 <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
375 <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 540 <output name="out" value="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
376 <param name="out_type" value="tsv"/> 541 <param name="out_type" value="tsv"/>
377 <section name="algorithm"> 542 <section name="algorithm">
378 <param name="retentionTimeInterpretation" value="iRT"/> 543 <param name="retentionTimeInterpretation" value="iRT"/>
379 <param name="override_group_label_check" value="true"/> 544 <param name="override_group_label_check" value="true"/>
380 <param name="force_invalid_mods" value="false"/> 545 <param name="force_invalid_mods" value="false"/>
383 <output name="ctd_out" ftype="xml"> 548 <output name="ctd_out" ftype="xml">
384 <assert_contents> 549 <assert_contents>
385 <is_valid_xml/> 550 <is_valid_xml/>
386 </assert_contents> 551 </assert_contents>
387 </output> 552 </output>
553 <assert_stdout>
554 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
555 </assert_stdout>
556 </test>
557 <!-- TOPP_TargetedFileConverter_test_9_prepare -->
558 <test expect_num_outputs="2">
559 <section name="adv_opts">
560 <param name="legacy_traml_id" value="false"/>
561 <param name="force" value="false"/>
562 <param name="test" value="true"/>
563 </section>
564 <param name="in" value="TargetedFileConverter_9_input.TraML"/>
565 <output name="out" value="TargetedFileConverter_9_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
566 <param name="out_type" value="pqp"/>
567 <section name="algorithm">
568 <param name="retentionTimeInterpretation" value="iRT"/>
569 <param name="override_group_label_check" value="true"/>
570 <param name="force_invalid_mods" value="false"/>
571 </section>
572 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
573 <output name="ctd_out" ftype="xml">
574 <assert_contents>
575 <is_valid_xml/>
576 </assert_contents>
577 </output>
578 <assert_stdout>
579 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
580 </assert_stdout>
388 </test> 581 </test>
389 <!-- TOPP_TargetedFileConverter_test_9 --> 582 <!-- TOPP_TargetedFileConverter_test_9 -->
390 <test expect_num_outputs="2"> 583 <test expect_num_outputs="2">
391 <section name="adv_opts"> 584 <section name="adv_opts">
392 <param name="legacy_traml_id" value="false"/> 585 <param name="legacy_traml_id" value="false"/>
393 <param name="force" value="false"/> 586 <param name="force" value="false"/>
394 <param name="test" value="true"/> 587 <param name="test" value="true"/>
395 </section> 588 </section>
396 <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> 589 <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
397 <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 590 <output name="out" value="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
398 <param name="out_type" value="TraML"/> 591 <param name="out_type" value="TraML"/>
399 <section name="algorithm"> 592 <section name="algorithm">
400 <param name="retentionTimeInterpretation" value="iRT"/> 593 <param name="retentionTimeInterpretation" value="iRT"/>
401 <param name="override_group_label_check" value="true"/> 594 <param name="override_group_label_check" value="true"/>
402 <param name="force_invalid_mods" value="false"/> 595 <param name="force_invalid_mods" value="false"/>
405 <output name="ctd_out" ftype="xml"> 598 <output name="ctd_out" ftype="xml">
406 <assert_contents> 599 <assert_contents>
407 <is_valid_xml/> 600 <is_valid_xml/>
408 </assert_contents> 601 </assert_contents>
409 </output> 602 </output>
603 <assert_stdout>
604 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
605 </assert_stdout>
410 </test> 606 </test>
411 <!-- TOPP_TargetedFileConverter_test_5 --> 607 <!-- TOPP_TargetedFileConverter_test_5 -->
412 <test expect_num_outputs="2"> 608 <test expect_num_outputs="2">
413 <section name="adv_opts"> 609 <section name="adv_opts">
414 <param name="legacy_traml_id" value="false"/> 610 <param name="legacy_traml_id" value="false"/>
415 <param name="force" value="false"/> 611 <param name="force" value="false"/>
416 <param name="test" value="true"/> 612 <param name="test" value="true"/>
417 </section> 613 </section>
418 <param name="in" value="ConvertTSVToTraML_output.TraML"/> 614 <param name="in" value="ConvertTSVToTraML_output.TraML"/>
419 <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 615 <output name="out" value="ConvertTraMLToTSV_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
420 <param name="out_type" value="tsv"/> 616 <param name="out_type" value="tsv"/>
421 <section name="algorithm"> 617 <section name="algorithm">
422 <param name="retentionTimeInterpretation" value="iRT"/> 618 <param name="retentionTimeInterpretation" value="iRT"/>
423 <param name="override_group_label_check" value="false"/> 619 <param name="override_group_label_check" value="false"/>
424 <param name="force_invalid_mods" value="false"/> 620 <param name="force_invalid_mods" value="false"/>
427 <output name="ctd_out" ftype="xml"> 623 <output name="ctd_out" ftype="xml">
428 <assert_contents> 624 <assert_contents>
429 <is_valid_xml/> 625 <is_valid_xml/>
430 </assert_contents> 626 </assert_contents>
431 </output> 627 </output>
628 <assert_stdout>
629 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
630 </assert_stdout>
631 </test>
632 <!-- TOPP_TargetedFileConverter_test_12_prepare -->
633 <test expect_num_outputs="2">
634 <section name="adv_opts">
635 <param name="legacy_traml_id" value="false"/>
636 <param name="force" value="false"/>
637 <param name="test" value="true"/>
638 </section>
639 <param name="in" value="TargetedFileConverter_12_input.TraML"/>
640 <output name="out" value="TargetedFileConverter_12_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
641 <param name="out_type" value="pqp"/>
642 <section name="algorithm">
643 <param name="retentionTimeInterpretation" value="iRT"/>
644 <param name="override_group_label_check" value="true"/>
645 <param name="force_invalid_mods" value="false"/>
646 </section>
647 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
648 <output name="ctd_out" ftype="xml">
649 <assert_contents>
650 <is_valid_xml/>
651 </assert_contents>
652 </output>
653 <assert_stdout>
654 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
655 </assert_stdout>
432 </test> 656 </test>
433 <!-- TOPP_TargetedFileConverter_test_12 --> 657 <!-- TOPP_TargetedFileConverter_test_12 -->
434 <test expect_num_outputs="2"> 658 <test expect_num_outputs="2">
435 <section name="adv_opts"> 659 <section name="adv_opts">
436 <param name="legacy_traml_id" value="false"/> 660 <param name="legacy_traml_id" value="false"/>
437 <param name="force" value="false"/> 661 <param name="force" value="false"/>
438 <param name="test" value="true"/> 662 <param name="test" value="true"/>
439 </section> 663 </section>
440 <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> 664 <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
441 <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 665 <output name="out" value="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
442 <param name="out_type" value="TraML"/> 666 <param name="out_type" value="TraML"/>
443 <section name="algorithm"> 667 <section name="algorithm">
444 <param name="retentionTimeInterpretation" value="iRT"/> 668 <param name="retentionTimeInterpretation" value="iRT"/>
445 <param name="override_group_label_check" value="true"/> 669 <param name="override_group_label_check" value="true"/>
446 <param name="force_invalid_mods" value="false"/> 670 <param name="force_invalid_mods" value="false"/>
449 <output name="ctd_out" ftype="xml"> 673 <output name="ctd_out" ftype="xml">
450 <assert_contents> 674 <assert_contents>
451 <is_valid_xml/> 675 <is_valid_xml/>
452 </assert_contents> 676 </assert_contents>
453 </output> 677 </output>
678 <assert_stdout>
679 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
680 </assert_stdout>
454 </test> 681 </test>
455 <!-- TOPP_TargetedFileConverter_test_13 --> 682 <!-- TOPP_TargetedFileConverter_test_13 -->
456 <test expect_num_outputs="2"> 683 <test expect_num_outputs="2">
457 <section name="adv_opts"> 684 <section name="adv_opts">
458 <param name="legacy_traml_id" value="false"/> 685 <param name="legacy_traml_id" value="false"/>
459 <param name="force" value="false"/> 686 <param name="force" value="false"/>
460 <param name="test" value="true"/> 687 <param name="test" value="true"/>
461 </section> 688 </section>
462 <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> 689 <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
463 <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 690 <output name="out" value="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
464 <param name="out_type" value="TraML"/> 691 <param name="out_type" value="TraML"/>
465 <section name="algorithm"> 692 <section name="algorithm">
466 <param name="retentionTimeInterpretation" value="iRT"/> 693 <param name="retentionTimeInterpretation" value="iRT"/>
467 <param name="override_group_label_check" value="false"/> 694 <param name="override_group_label_check" value="false"/>
468 <param name="force_invalid_mods" value="false"/> 695 <param name="force_invalid_mods" value="false"/>
469 </section> 696 </section>
470 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 697 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
471 <output name="ctd_out" ftype="xml"> 698 <output name="ctd_out" ftype="xml">
472 <assert_contents> 699 <assert_contents>
473 <is_valid_xml/> 700 <is_valid_xml/>
474 </assert_contents> 701 </assert_contents>
475 </output> 702 </output>
703 <assert_stdout>
704 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
705 </assert_stdout>
476 </test> 706 </test>
477 <!-- TOPP_TargetedFileConverter_test_6 --> 707 <!-- TOPP_TargetedFileConverter_test_6 -->
478 <test expect_num_outputs="2"> 708 <test expect_num_outputs="2">
479 <section name="adv_opts"> 709 <section name="adv_opts">
480 <param name="legacy_traml_id" value="false"/> 710 <param name="legacy_traml_id" value="false"/>
481 <param name="force" value="false"/> 711 <param name="force" value="false"/>
482 <param name="test" value="true"/> 712 <param name="test" value="true"/>
483 </section> 713 </section>
484 <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> 714 <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
485 <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 715 <output name="out" value="ConvertTraMLToTSV_output_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
486 <param name="out_type" value="tsv"/> 716 <param name="out_type" value="tsv"/>
487 <section name="algorithm"> 717 <section name="algorithm">
488 <param name="retentionTimeInterpretation" value="iRT"/> 718 <param name="retentionTimeInterpretation" value="iRT"/>
489 <param name="override_group_label_check" value="false"/> 719 <param name="override_group_label_check" value="false"/>
490 <param name="force_invalid_mods" value="false"/> 720 <param name="force_invalid_mods" value="false"/>
493 <output name="ctd_out" ftype="xml"> 723 <output name="ctd_out" ftype="xml">
494 <assert_contents> 724 <assert_contents>
495 <is_valid_xml/> 725 <is_valid_xml/>
496 </assert_contents> 726 </assert_contents>
497 </output> 727 </output>
498 </test> 728 <assert_stdout>
499 <!-- UTILS_AssayGeneratorMetabo_6 --> 729 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
730 </assert_stdout>
731 </test>
732 <!-- TOPP_OpenSwathWorkflow_13_prepare -->
733 <test expect_num_outputs="2">
734 <section name="adv_opts">
735 <param name="legacy_traml_id" value="false"/>
736 <param name="force" value="false"/>
737 <param name="test" value="true"/>
738 </section>
739 <param name="in" value="OpenSwathWorkflow_1_input.TraML"/>
740 <output name="out" value="OpenSwathWorkflow_13_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
741 <param name="out_type" value="pqp"/>
742 <section name="algorithm">
743 <param name="retentionTimeInterpretation" value="iRT"/>
744 <param name="override_group_label_check" value="false"/>
745 <param name="force_invalid_mods" value="false"/>
746 </section>
747 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
748 <output name="ctd_out" ftype="xml">
749 <assert_contents>
750 <is_valid_xml/>
751 </assert_contents>
752 </output>
753 <assert_stdout>
754 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
755 </assert_stdout>
756 </test>
757 <!-- TOPP_OpenSwathWorkflow_14_prepare -->
758 <test expect_num_outputs="2">
759 <section name="adv_opts">
760 <param name="legacy_traml_id" value="false"/>
761 <param name="force" value="false"/>
762 <param name="test" value="true"/>
763 </section>
764 <param name="in" value="OpenSwathWorkflow_1_input.TraML"/>
765 <output name="out" value="OpenSwathWorkflow_14_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
766 <param name="out_type" value="pqp"/>
767 <section name="algorithm">
768 <param name="retentionTimeInterpretation" value="iRT"/>
769 <param name="override_group_label_check" value="false"/>
770 <param name="force_invalid_mods" value="false"/>
771 </section>
772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
773 <output name="ctd_out" ftype="xml">
774 <assert_contents>
775 <is_valid_xml/>
776 </assert_contents>
777 </output>
778 <assert_stdout>
779 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
780 </assert_stdout>
781 </test>
782 <!-- TOPP_OpenSwathWorkflow_17_b_prepare -->
783 <test expect_num_outputs="2">
784 <section name="adv_opts">
785 <param name="legacy_traml_id" value="false"/>
786 <param name="force" value="false"/>
787 <param name="test" value="true"/>
788 </section>
789 <param name="in" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
790 <output name="out" value="OpenSwathWorkflow_17_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
791 <param name="out_type" value="pqp"/>
792 <section name="algorithm">
793 <param name="retentionTimeInterpretation" value="iRT"/>
794 <param name="override_group_label_check" value="false"/>
795 <param name="force_invalid_mods" value="false"/>
796 </section>
797 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
798 <output name="ctd_out" ftype="xml">
799 <assert_contents>
800 <is_valid_xml/>
801 </assert_contents>
802 </output>
803 <assert_stdout>
804 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
805 </assert_stdout>
806 </test>
807 <!-- TOPP_AssayGeneratorMetabo_6 -->
500 <test expect_num_outputs="2"> 808 <test expect_num_outputs="2">
501 <section name="adv_opts"> 809 <section name="adv_opts">
502 <param name="legacy_traml_id" value="false"/> 810 <param name="legacy_traml_id" value="false"/>
503 <param name="force" value="false"/> 811 <param name="force" value="false"/>
504 <param name="test" value="true"/> 812 <param name="test" value="true"/>
505 </section> 813 </section>
506 <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> 814 <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
507 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 815 <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus_traml.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
508 <param name="out_type" value="TraML"/> 816 <param name="out_type" value="TraML"/>
509 <section name="algorithm"> 817 <section name="algorithm">
510 <param name="retentionTimeInterpretation" value="iRT"/> 818 <param name="retentionTimeInterpretation" value="iRT"/>
511 <param name="override_group_label_check" value="false"/> 819 <param name="override_group_label_check" value="false"/>
512 <param name="force_invalid_mods" value="false"/> 820 <param name="force_invalid_mods" value="false"/>
513 </section> 821 </section>
514 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 822 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
515 <output name="ctd_out" ftype="xml"> 823 <output name="ctd_out" ftype="xml">
516 <assert_contents> 824 <assert_contents>
517 <is_valid_xml/> 825 <is_valid_xml/>
518 </assert_contents> 826 </assert_contents>
519 </output> 827 </output>
828 <assert_stdout>
829 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
830 </assert_stdout>
520 </test> 831 </test>
521 </tests> 832 </tests>
522 <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis. 833 <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.
523 834
524 835
525 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TargetedFileConverter.html]]></help> 836 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TargetedFileConverter.html]]></help>
526 <expand macro="references"/> 837 <expand macro="references"/>
527 </tool> 838 </tool>