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comparison TextExporter.xml @ 14:b5de4c3efbdd 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 21:44:36 +0000
parents 1b03536aa3c9
children
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13:1b03536aa3c9 14:b5de4c3efbdd
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: [File Handling]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Exports various XML formats to a text file.</description> 4 <description>Exports various XML formats to a text file</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">TextExporter</token> 6 <token name="@EXECUTABLE@">TextExporter</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($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir consensus_centroids && 20 mkdir consensus_centroids &&
22 #end if 21 #end if
23 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 22 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
70 <configfiles> 69 <configfiles>
71 <inputs name="args_json" data_style="paths"/> 70 <inputs name="args_json" data_style="paths"/>
72 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 71 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
73 </configfiles> 72 </configfiles>
74 <inputs> 73 <inputs>
75 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/> 74 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
76 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help=""> 75 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
77 <option value="csv">csv</option> 76 <option value="csv">csv</option>
78 <option value="tsv">tabular (tsv)</option> 77 <option value="tsv">tabular (tsv)</option>
79 <option value="txt">txt</option> 78 <option value="txt">txt</option>
79 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
80 <expand macro="list_string_san" name="out_type"/> 80 <expand macro="list_string_san" name="out_type"/>
81 </param> 81 </param>
82 <param argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help=""> 82 <param argument="-replacement" type="text" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
83 <expand macro="list_string_san" name="replacement"/> 83 <expand macro="list_string_san" name="replacement"/>
84 </param> 84 </param>
85 <param argument="-quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> 85 <param argument="-quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
86 <option value="none" selected="true">none</option> 86 <option value="none" selected="true">none</option>
87 <option value="double">double</option> 87 <option value="double">double</option>
88 <option value="escape">escape</option> 88 <option value="escape">escape</option>
89 <expand macro="list_string_san" name="quoting"/> 89 <expand macro="list_string_san" name="quoting"/>
90 </param> 90 </param>
91 <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/> 91 <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/>
92 <section name="feature" title="Options for featureXML input files" help="" expanded="false"> 92 <section name="feature" title="Options for featureXML input files" help="" expanded="false">
93 <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/> 93 <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/>
94 <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> 94 <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
95 </section> 95 </section>
96 <section name="id" title="Options for idXML input files" help="" expanded="false"> 96 <section name="id" title="Options for idXML input files" help="" expanded="false">
97 <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/> 97 <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/>
98 <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/> 98 <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/>
99 <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/> 99 <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/>
100 <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/> 100 <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/>
101 <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> 101 <param name="add_metavalues" argument="-id:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
102 <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> 102 <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
103 <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> 103 <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
104 </section> 104 </section>
105 <section name="consensus" title="Options for consensusXML input files" help="" expanded="false"> 105 <section name="consensus" title="Options for consensusXML input files" help="" expanded="false">
106 <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="true" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method"> 106 <param name="sorting_method" argument="-consensus:sorting_method" type="select" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
107 <option value="none" selected="true">none</option> 107 <option value="none" selected="true">none</option>
108 <option value="RT">RT</option> 108 <option value="RT">RT</option>
109 <option value="MZ">MZ</option> 109 <option value="MZ">MZ</option>
110 <option value="RT_then_MZ">RT_then_MZ</option> 110 <option value="RT_then_MZ">RT_then_MZ</option>
111 <option value="intensity">intensity</option> 111 <option value="intensity">intensity</option>
113 <option value="quality_increasing">quality_increasing</option> 113 <option value="quality_increasing">quality_increasing</option>
114 <expand macro="list_string_san" name="sorting_method"/> 114 <expand macro="list_string_san" name="sorting_method"/>
115 </param> 115 </param>
116 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/> 116 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/>
117 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/> 117 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
118 <param name="add_metavalues" argument="-consensus:add_metavalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add columns for ConsensusFeature meta values" help=""/>
118 </section> 119 </section>
119 <expand macro="adv_opts_macro"> 120 <expand macro="adv_opts_macro">
120 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 121 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
121 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 122 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
122 <expand macro="list_string_san" name="test"/> 123 <expand macro="list_string_san" name="test"/>
123 </param> 124 </param>
124 </expand> 125 </expand>
125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
126 <option value="centroids_FLAG">centroids (Output file for centroids of consensus features)</option> 127 <option value="centroids_FLAG">centroids (Output file for centroids of consensus features)</option>
147 </data> 148 </data>
148 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
149 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
150 </data> 151 </data>
151 </outputs> 152 </outputs>
152 <tests><!-- TOPP_TextExporter_1 --> 153 <tests>
154 <!-- TOPP_TextExporter_1 -->
153 <test expect_num_outputs="2"> 155 <test expect_num_outputs="2">
154 <section name="adv_opts"> 156 <section name="adv_opts">
155 <param name="force" value="false"/> 157 <param name="force" value="false"/>
156 <param name="test" value="true"/> 158 <param name="test" value="true"/>
157 </section> 159 </section>
158 <param name="in" value="TextExporter_1_input.featureXML"/> 160 <param name="in" value="TextExporter_1_input.featureXML"/>
159 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 161 <output name="out" value="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
160 <param name="out_type" value="txt"/> 162 <param name="out_type" value="txt"/>
161 <param name="replacement" value="_"/> 163 <param name="replacement" value="_"/>
162 <param name="quoting" value="none"/> 164 <param name="quoting" value="none"/>
163 <param name="no_ids" value="false"/> 165 <param name="no_ids" value="false"/>
164 <section name="feature"> 166 <section name="feature">
176 </section> 178 </section>
177 <section name="consensus"> 179 <section name="consensus">
178 <param name="sorting_method" value="none"/> 180 <param name="sorting_method" value="none"/>
179 <param name="sort_by_maps" value="false"/> 181 <param name="sort_by_maps" value="false"/>
180 <param name="sort_by_size" value="false"/> 182 <param name="sort_by_size" value="false"/>
181 </section> 183 <param name="add_metavalues" value="false"/>
182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 184 </section>
183 <output name="ctd_out" ftype="xml"> 185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
184 <assert_contents> 186 <output name="ctd_out" ftype="xml">
185 <is_valid_xml/> 187 <assert_contents>
186 </assert_contents> 188 <is_valid_xml/>
187 </output> 189 </assert_contents>
190 </output>
191 <assert_stdout>
192 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
193 </assert_stdout>
188 </test> 194 </test>
189 <!-- TOPP_TextExporter_2 --> 195 <!-- TOPP_TextExporter_2 -->
190 <test expect_num_outputs="5"> 196 <test expect_num_outputs="5">
191 <section name="adv_opts"> 197 <section name="adv_opts">
192 <param name="force" value="false"/> 198 <param name="force" value="false"/>
193 <param name="test" value="true"/> 199 <param name="test" value="true"/>
194 </section> 200 </section>
195 <param name="in" value="TextExporter_2_input.consensusXML"/> 201 <param name="in" value="TextExporter_2_input.consensusXML"/>
196 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 202 <output name="out" value="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
197 <param name="out_type" value="tsv"/> 203 <param name="out_type" value="tsv"/>
198 <param name="replacement" value="_"/> 204 <param name="replacement" value="_"/>
199 <param name="quoting" value="none"/> 205 <param name="quoting" value="none"/>
200 <param name="no_ids" value="true"/> 206 <param name="no_ids" value="true"/>
201 <section name="feature"> 207 <section name="feature">
213 </section> 219 </section>
214 <section name="consensus"> 220 <section name="consensus">
215 <param name="sorting_method" value="RT_then_MZ"/> 221 <param name="sorting_method" value="RT_then_MZ"/>
216 <param name="sort_by_maps" value="true"/> 222 <param name="sort_by_maps" value="true"/>
217 <param name="sort_by_size" value="true"/> 223 <param name="sort_by_size" value="true"/>
218 </section> 224 <param name="add_metavalues" value="true"/>
219 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> 225 </section>
220 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> 226 <output name="consensus_centroids" value="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
221 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> 227 <output name="consensus_elements" value="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
228 <output name="consensus_features" value="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
222 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> 229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
223 <output name="ctd_out" ftype="xml"> 230 <output name="ctd_out" ftype="xml">
224 <assert_contents> 231 <assert_contents>
225 <is_valid_xml/> 232 <is_valid_xml/>
226 </assert_contents> 233 </assert_contents>
227 </output> 234 </output>
235 <assert_stdout>
236 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
237 </assert_stdout>
228 </test> 238 </test>
229 <!-- TOPP_TextExporter_3 --> 239 <!-- TOPP_TextExporter_3 -->
230 <test expect_num_outputs="2"> 240 <test expect_num_outputs="2">
231 <section name="adv_opts"> 241 <section name="adv_opts">
232 <param name="force" value="false"/> 242 <param name="force" value="false"/>
233 <param name="test" value="true"/> 243 <param name="test" value="true"/>
234 </section> 244 </section>
235 <param name="in" value="TextExporter_3_input.idXML"/> 245 <param name="in" value="TextExporter_3_input.idXML"/>
236 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 246 <output name="out" value="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
237 <param name="out_type" value="txt"/> 247 <param name="out_type" value="txt"/>
238 <param name="replacement" value="_"/> 248 <param name="replacement" value="_"/>
239 <param name="quoting" value="none"/> 249 <param name="quoting" value="none"/>
240 <param name="no_ids" value="false"/> 250 <param name="no_ids" value="false"/>
241 <section name="feature"> 251 <section name="feature">
253 </section> 263 </section>
254 <section name="consensus"> 264 <section name="consensus">
255 <param name="sorting_method" value="none"/> 265 <param name="sorting_method" value="none"/>
256 <param name="sort_by_maps" value="false"/> 266 <param name="sort_by_maps" value="false"/>
257 <param name="sort_by_size" value="false"/> 267 <param name="sort_by_size" value="false"/>
258 </section> 268 <param name="add_metavalues" value="false"/>
259 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 269 </section>
260 <output name="ctd_out" ftype="xml"> 270 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
261 <assert_contents> 271 <output name="ctd_out" ftype="xml">
262 <is_valid_xml/> 272 <assert_contents>
263 </assert_contents> 273 <is_valid_xml/>
264 </output> 274 </assert_contents>
275 </output>
276 <assert_stdout>
277 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
278 </assert_stdout>
265 </test> 279 </test>
266 <!-- TOPP_TextExporter_4 --> 280 <!-- TOPP_TextExporter_4 -->
267 <test expect_num_outputs="2"> 281 <test expect_num_outputs="2">
268 <section name="adv_opts"> 282 <section name="adv_opts">
269 <param name="force" value="false"/> 283 <param name="force" value="false"/>
270 <param name="test" value="true"/> 284 <param name="test" value="true"/>
271 </section> 285 </section>
272 <param name="in" value="TextExporter_3_input.idXML"/> 286 <param name="in" value="TextExporter_3_input.idXML"/>
273 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 287 <output name="out" value="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
274 <param name="out_type" value="txt"/> 288 <param name="out_type" value="txt"/>
275 <param name="replacement" value="_"/> 289 <param name="replacement" value="_"/>
276 <param name="quoting" value="none"/> 290 <param name="quoting" value="none"/>
277 <param name="no_ids" value="false"/> 291 <param name="no_ids" value="false"/>
278 <section name="feature"> 292 <section name="feature">
290 </section> 304 </section>
291 <section name="consensus"> 305 <section name="consensus">
292 <param name="sorting_method" value="none"/> 306 <param name="sorting_method" value="none"/>
293 <param name="sort_by_maps" value="false"/> 307 <param name="sort_by_maps" value="false"/>
294 <param name="sort_by_size" value="false"/> 308 <param name="sort_by_size" value="false"/>
295 </section> 309 <param name="add_metavalues" value="false"/>
296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 310 </section>
297 <output name="ctd_out" ftype="xml"> 311 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
298 <assert_contents> 312 <output name="ctd_out" ftype="xml">
299 <is_valid_xml/> 313 <assert_contents>
300 </assert_contents> 314 <is_valid_xml/>
301 </output> 315 </assert_contents>
316 </output>
317 <assert_stdout>
318 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
319 </assert_stdout>
302 </test> 320 </test>
303 <!-- TOPP_TextExporter_5 --> 321 <!-- TOPP_TextExporter_5 -->
304 <test expect_num_outputs="2"> 322 <test expect_num_outputs="2">
305 <section name="adv_opts"> 323 <section name="adv_opts">
306 <param name="force" value="false"/> 324 <param name="force" value="false"/>
307 <param name="test" value="true"/> 325 <param name="test" value="true"/>
308 </section> 326 </section>
309 <param name="in" value="TextExporter_5_input.idXML"/> 327 <param name="in" value="TextExporter_5_input.idXML"/>
310 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 328 <output name="out" value="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
311 <param name="out_type" value="txt"/> 329 <param name="out_type" value="txt"/>
312 <param name="replacement" value="_"/> 330 <param name="replacement" value="_"/>
313 <param name="quoting" value="none"/> 331 <param name="quoting" value="none"/>
314 <param name="no_ids" value="false"/> 332 <param name="no_ids" value="false"/>
315 <section name="feature"> 333 <section name="feature">
327 </section> 345 </section>
328 <section name="consensus"> 346 <section name="consensus">
329 <param name="sorting_method" value="none"/> 347 <param name="sorting_method" value="none"/>
330 <param name="sort_by_maps" value="false"/> 348 <param name="sort_by_maps" value="false"/>
331 <param name="sort_by_size" value="false"/> 349 <param name="sort_by_size" value="false"/>
332 </section> 350 <param name="add_metavalues" value="false"/>
333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 351 </section>
334 <output name="ctd_out" ftype="xml"> 352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
335 <assert_contents> 353 <output name="ctd_out" ftype="xml">
336 <is_valid_xml/> 354 <assert_contents>
337 </assert_contents> 355 <is_valid_xml/>
338 </output> 356 </assert_contents>
357 </output>
358 <assert_stdout>
359 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
360 </assert_stdout>
339 </test> 361 </test>
340 <!-- TOPP_TextExporter_6 --> 362 <!-- TOPP_TextExporter_6 -->
341 <test expect_num_outputs="2"> 363 <test expect_num_outputs="2">
342 <section name="adv_opts"> 364 <section name="adv_opts">
343 <param name="force" value="false"/> 365 <param name="force" value="false"/>
344 <param name="test" value="true"/> 366 <param name="test" value="true"/>
345 </section> 367 </section>
346 <param name="in" value="TextExporter_6_input.featureXML"/> 368 <param name="in" value="TextExporter_6_input.featureXML"/>
347 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 369 <output name="out" value="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
348 <param name="out_type" value="txt"/> 370 <param name="out_type" value="txt"/>
349 <param name="replacement" value="_"/> 371 <param name="replacement" value="_"/>
350 <param name="quoting" value="none"/> 372 <param name="quoting" value="none"/>
351 <param name="no_ids" value="true"/> 373 <param name="no_ids" value="true"/>
352 <section name="feature"> 374 <section name="feature">
364 </section> 386 </section>
365 <section name="consensus"> 387 <section name="consensus">
366 <param name="sorting_method" value="none"/> 388 <param name="sorting_method" value="none"/>
367 <param name="sort_by_maps" value="false"/> 389 <param name="sort_by_maps" value="false"/>
368 <param name="sort_by_size" value="false"/> 390 <param name="sort_by_size" value="false"/>
369 </section> 391 <param name="add_metavalues" value="false"/>
370 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 392 </section>
371 <output name="ctd_out" ftype="xml"> 393 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
372 <assert_contents> 394 <output name="ctd_out" ftype="xml">
373 <is_valid_xml/> 395 <assert_contents>
374 </assert_contents> 396 <is_valid_xml/>
375 </output> 397 </assert_contents>
398 </output>
399 <assert_stdout>
400 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
401 </assert_stdout>
376 </test> 402 </test>
377 <!-- TOPP_TextExporter_7 --> 403 <!-- TOPP_TextExporter_7 -->
378 <test expect_num_outputs="2"> 404 <test expect_num_outputs="2">
379 <section name="adv_opts"> 405 <section name="adv_opts">
380 <param name="force" value="false"/> 406 <param name="force" value="false"/>
381 <param name="test" value="true"/> 407 <param name="test" value="true"/>
382 </section> 408 </section>
383 <param name="in" value="TextExporter_7_input.consensusXML"/> 409 <param name="in" value="TextExporter_7_input.consensusXML"/>
384 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> 410 <output name="out" value="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
385 <param name="out_type" value="tsv"/> 411 <param name="out_type" value="tsv"/>
386 <param name="replacement" value="_"/> 412 <param name="replacement" value="_"/>
387 <param name="quoting" value="none"/> 413 <param name="quoting" value="none"/>
388 <param name="no_ids" value="false"/> 414 <param name="no_ids" value="false"/>
389 <section name="feature"> 415 <section name="feature">
401 </section> 427 </section>
402 <section name="consensus"> 428 <section name="consensus">
403 <param name="sorting_method" value="RT_then_MZ"/> 429 <param name="sorting_method" value="RT_then_MZ"/>
404 <param name="sort_by_maps" value="true"/> 430 <param name="sort_by_maps" value="true"/>
405 <param name="sort_by_size" value="true"/> 431 <param name="sort_by_size" value="true"/>
406 </section> 432 <param name="add_metavalues" value="false"/>
407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 433 </section>
408 <output name="ctd_out" ftype="xml"> 434 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
409 <assert_contents> 435 <output name="ctd_out" ftype="xml">
410 <is_valid_xml/> 436 <assert_contents>
411 </assert_contents> 437 <is_valid_xml/>
412 </output> 438 </assert_contents>
439 </output>
440 <assert_stdout>
441 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
442 </assert_stdout>
413 </test> 443 </test>
414 <!-- TOPP_TextExporter_8 --> 444 <!-- TOPP_TextExporter_8 -->
415 <test expect_num_outputs="2"> 445 <test expect_num_outputs="2">
416 <section name="adv_opts"> 446 <section name="adv_opts">
417 <param name="force" value="false"/> 447 <param name="force" value="false"/>
418 <param name="test" value="true"/> 448 <param name="test" value="true"/>
419 </section> 449 </section>
420 <param name="in" value="TextExporter_1_input.featureXML"/> 450 <param name="in" value="TextExporter_1_input.featureXML"/>
421 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 451 <output name="out" value="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
422 <param name="out_type" value="txt"/> 452 <param name="out_type" value="txt"/>
423 <param name="replacement" value="_"/> 453 <param name="replacement" value="_"/>
424 <param name="quoting" value="none"/> 454 <param name="quoting" value="none"/>
425 <param name="no_ids" value="true"/> 455 <param name="no_ids" value="true"/>
426 <section name="feature"> 456 <section name="feature">
438 </section> 468 </section>
439 <section name="consensus"> 469 <section name="consensus">
440 <param name="sorting_method" value="none"/> 470 <param name="sorting_method" value="none"/>
441 <param name="sort_by_maps" value="false"/> 471 <param name="sort_by_maps" value="false"/>
442 <param name="sort_by_size" value="false"/> 472 <param name="sort_by_size" value="false"/>
443 </section> 473 <param name="add_metavalues" value="false"/>
444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 474 </section>
445 <output name="ctd_out" ftype="xml"> 475 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
446 <assert_contents> 476 <output name="ctd_out" ftype="xml">
447 <is_valid_xml/> 477 <assert_contents>
448 </assert_contents> 478 <is_valid_xml/>
449 </output> 479 </assert_contents>
480 </output>
481 <assert_stdout>
482 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
483 </assert_stdout>
450 </test> 484 </test>
451 <!-- TOPP_TextExporter_9 --> 485 <!-- TOPP_TextExporter_9 -->
452 <test expect_num_outputs="2"> 486 <test expect_num_outputs="2">
453 <section name="adv_opts"> 487 <section name="adv_opts">
454 <param name="force" value="false"/> 488 <param name="force" value="false"/>
455 <param name="test" value="true"/> 489 <param name="test" value="true"/>
456 </section> 490 </section>
457 <param name="in" value="TextExporter_9_input.idXML"/> 491 <param name="in" value="TextExporter_9_input.idXML"/>
458 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 492 <output name="out" value="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
459 <param name="out_type" value="txt"/> 493 <param name="out_type" value="txt"/>
460 <param name="replacement" value="_"/> 494 <param name="replacement" value="_"/>
461 <param name="quoting" value="none"/> 495 <param name="quoting" value="none"/>
462 <param name="no_ids" value="false"/> 496 <param name="no_ids" value="false"/>
463 <section name="feature"> 497 <section name="feature">
475 </section> 509 </section>
476 <section name="consensus"> 510 <section name="consensus">
477 <param name="sorting_method" value="none"/> 511 <param name="sorting_method" value="none"/>
478 <param name="sort_by_maps" value="false"/> 512 <param name="sort_by_maps" value="false"/>
479 <param name="sort_by_size" value="false"/> 513 <param name="sort_by_size" value="false"/>
480 </section> 514 <param name="add_metavalues" value="false"/>
481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 515 </section>
482 <output name="ctd_out" ftype="xml"> 516 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
483 <assert_contents> 517 <output name="ctd_out" ftype="xml">
484 <is_valid_xml/> 518 <assert_contents>
485 </assert_contents> 519 <is_valid_xml/>
486 </output> 520 </assert_contents>
521 </output>
522 <assert_stdout>
523 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
524 </assert_stdout>
487 </test> 525 </test>
488 </tests> 526 </tests>
489 <help><![CDATA[Exports various XML formats to a text file. 527 <help><![CDATA[Exports various XML formats to a text file.
490 528
491 529
492 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TextExporter.html]]></help> 530 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TextExporter.html]]></help>
493 <expand macro="references"/> 531 <expand macro="references"/>
494 </tool> 532 </tool>