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comparison FileInfo.xml @ 16:5a45e6ac9aae 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 21:32:58 +0000
parents 4af67edd5aef
children
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15:4af67edd5aef 16:5a45e6ac9aae
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 Filtering / Extraction / Merging]-->
4 <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Shows basic information about the file, such as data ranges and file type.</description> 4 <description>Shows basic information about the file, such as data ranges and file type</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FileInfo</token> 6 <token name="@EXECUTABLE@">FileInfo</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir out_tsv && 20 mkdir out_tsv &&
22 #end if 21 #end if
23 22
50 <configfiles> 49 <configfiles>
51 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
53 </configfiles> 52 </configfiles>
54 <inputs> 53 <inputs>
55 <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/> 54 <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/>
56 <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> 55 <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
57 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> 56 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
58 <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/> 57 <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
59 <param argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/> 58 <param argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
60 <param argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/> 59 <param argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
61 <param argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/> 60 <param argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
62 <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/> 61 <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
63 <expand macro="adv_opts_macro"> 62 <expand macro="adv_opts_macro">
64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 63 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
65 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 64 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
66 <expand macro="list_string_san" name="test"/> 65 <expand macro="list_string_san" name="test"/>
67 </param> 66 </param>
68 </expand> 67 </expand>
69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 68 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
70 <option value="out_tsv_FLAG">out_tsv (Second optional output file)</option> 69 <option value="out_tsv_FLAG">out_tsv (Second optional output file)</option>
78 </data> 77 </data>
79 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
80 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
81 </data> 80 </data>
82 </outputs> 81 </outputs>
83 <tests><!-- TOPP_FileInfo_1 --> 82 <tests>
83 <!-- TOPP_FileInfo_1 -->
84 <test expect_num_outputs="2"> 84 <test expect_num_outputs="2">
85 <section name="adv_opts"> 85 <section name="adv_opts">
86 <param name="force" value="false"/> 86 <param name="force" value="false"/>
87 <param name="test" value="true"/> 87 <param name="test" value="true"/>
88 </section> 88 </section>
89 <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> 89 <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
90 <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 90 <output name="out" value="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
91 <param name="m" value="false"/> 91 <param name="m" value="false"/>
92 <param name="p" value="false"/> 92 <param name="p" value="false"/>
93 <param name="s" value="false"/> 93 <param name="s" value="false"/>
94 <param name="d" value="false"/> 94 <param name="d" value="false"/>
95 <param name="c" value="false"/> 95 <param name="c" value="false"/>
96 <param name="v" value="false"/> 96 <param name="v" value="false"/>
97 <param name="i" value="false"/> 97 <param name="i" value="false"/>
98 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 98 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
99 <output name="ctd_out" ftype="xml"> 99 <output name="ctd_out" ftype="xml">
100 <assert_contents> 100 <assert_contents>
101 <is_valid_xml/> 101 <is_valid_xml/>
102 </assert_contents> 102 </assert_contents>
103 </output> 103 </output>
104 <assert_stdout>
105 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
106 </assert_stdout>
104 </test> 107 </test>
105 <!-- TOPP_FileInfo_2 --> 108 <!-- TOPP_FileInfo_2 -->
106 <test expect_num_outputs="2"> 109 <test expect_num_outputs="2">
107 <section name="adv_opts"> 110 <section name="adv_opts">
108 <param name="force" value="false"/> 111 <param name="force" value="false"/>
109 <param name="test" value="true"/> 112 <param name="test" value="true"/>
110 </section> 113 </section>
111 <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> 114 <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
112 <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 115 <output name="out" value="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
113 <param name="m" value="false"/> 116 <param name="m" value="false"/>
114 <param name="p" value="false"/> 117 <param name="p" value="false"/>
115 <param name="s" value="false"/> 118 <param name="s" value="false"/>
116 <param name="d" value="false"/> 119 <param name="d" value="false"/>
117 <param name="c" value="false"/> 120 <param name="c" value="false"/>
118 <param name="v" value="false"/> 121 <param name="v" value="false"/>
119 <param name="i" value="false"/> 122 <param name="i" value="false"/>
120 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
121 <output name="ctd_out" ftype="xml"> 124 <output name="ctd_out" ftype="xml">
122 <assert_contents> 125 <assert_contents>
123 <is_valid_xml/> 126 <is_valid_xml/>
124 </assert_contents> 127 </assert_contents>
125 </output> 128 </output>
129 <assert_stdout>
130 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
131 </assert_stdout>
126 </test> 132 </test>
127 <!-- TOPP_FileInfo_3 --> 133 <!-- TOPP_FileInfo_3 -->
128 <test expect_num_outputs="2"> 134 <test expect_num_outputs="2">
129 <section name="adv_opts"> 135 <section name="adv_opts">
130 <param name="force" value="false"/> 136 <param name="force" value="false"/>
131 <param name="test" value="true"/> 137 <param name="test" value="true"/>
132 </section> 138 </section>
133 <param name="in" value="FileInfo_3_input.featureXML"/> 139 <param name="in" value="FileInfo_3_input.featureXML"/>
134 <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 140 <output name="out" value="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
135 <param name="m" value="true"/> 141 <param name="m" value="true"/>
136 <param name="p" value="true"/> 142 <param name="p" value="true"/>
137 <param name="s" value="true"/> 143 <param name="s" value="true"/>
138 <param name="d" value="false"/> 144 <param name="d" value="false"/>
139 <param name="c" value="false"/> 145 <param name="c" value="false"/>
143 <output name="ctd_out" ftype="xml"> 149 <output name="ctd_out" ftype="xml">
144 <assert_contents> 150 <assert_contents>
145 <is_valid_xml/> 151 <is_valid_xml/>
146 </assert_contents> 152 </assert_contents>
147 </output> 153 </output>
154 <assert_stdout>
155 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
156 </assert_stdout>
148 </test> 157 </test>
149 <!-- TOPP_FileInfo_4 --> 158 <!-- TOPP_FileInfo_4 -->
150 <test expect_num_outputs="2"> 159 <test expect_num_outputs="2">
151 <section name="adv_opts"> 160 <section name="adv_opts">
152 <param name="force" value="false"/> 161 <param name="force" value="false"/>
153 <param name="test" value="true"/> 162 <param name="test" value="true"/>
154 </section> 163 </section>
155 <param name="in" value="FileInfo_4_input.mzXML"/> 164 <param name="in" value="FileInfo_4_input.mzXML"/>
156 <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 165 <output name="out" value="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
157 <param name="m" value="true"/> 166 <param name="m" value="true"/>
158 <param name="p" value="false"/> 167 <param name="p" value="false"/>
159 <param name="s" value="false"/> 168 <param name="s" value="false"/>
160 <param name="d" value="false"/> 169 <param name="d" value="false"/>
161 <param name="c" value="false"/> 170 <param name="c" value="false"/>
165 <output name="ctd_out" ftype="xml"> 174 <output name="ctd_out" ftype="xml">
166 <assert_contents> 175 <assert_contents>
167 <is_valid_xml/> 176 <is_valid_xml/>
168 </assert_contents> 177 </assert_contents>
169 </output> 178 </output>
179 <assert_stdout>
180 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
181 </assert_stdout>
170 </test> 182 </test>
171 <!-- TOPP_FileInfo_5 --> 183 <!-- TOPP_FileInfo_5 -->
172 <test expect_num_outputs="2"> 184 <test expect_num_outputs="2">
173 <section name="adv_opts"> 185 <section name="adv_opts">
174 <param name="force" value="false"/> 186 <param name="force" value="false"/>
175 <param name="test" value="true"/> 187 <param name="test" value="true"/>
176 </section> 188 </section>
177 <param name="in" value="FileInfo_5_input.mzDat"/> 189 <param name="in" value="FileInfo_5_input.mzDat"/>
178 <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 190 <output name="out" value="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
179 <param name="m" value="true"/> 191 <param name="m" value="true"/>
180 <param name="p" value="false"/> 192 <param name="p" value="false"/>
181 <param name="s" value="true"/> 193 <param name="s" value="true"/>
182 <param name="d" value="false"/> 194 <param name="d" value="false"/>
183 <param name="c" value="false"/> 195 <param name="c" value="false"/>
187 <output name="ctd_out" ftype="xml"> 199 <output name="ctd_out" ftype="xml">
188 <assert_contents> 200 <assert_contents>
189 <is_valid_xml/> 201 <is_valid_xml/>
190 </assert_contents> 202 </assert_contents>
191 </output> 203 </output>
204 <assert_stdout>
205 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
206 </assert_stdout>
192 </test> 207 </test>
193 <!-- TOPP_FileInfo_6 --> 208 <!-- TOPP_FileInfo_6 -->
194 <test expect_num_outputs="2"> 209 <test expect_num_outputs="2">
195 <section name="adv_opts"> 210 <section name="adv_opts">
196 <param name="force" value="false"/> 211 <param name="force" value="false"/>
197 <param name="test" value="true"/> 212 <param name="test" value="true"/>
198 </section> 213 </section>
199 <param name="in" value="FileInfo_6_input.mzData"/> 214 <param name="in" value="FileInfo_6_input.mzData"/>
200 <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 215 <output name="out" value="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
201 <param name="m" value="false"/> 216 <param name="m" value="false"/>
202 <param name="p" value="false"/> 217 <param name="p" value="false"/>
203 <param name="s" value="true"/> 218 <param name="s" value="true"/>
204 <param name="d" value="true"/> 219 <param name="d" value="true"/>
205 <param name="c" value="false"/> 220 <param name="c" value="false"/>
209 <output name="ctd_out" ftype="xml"> 224 <output name="ctd_out" ftype="xml">
210 <assert_contents> 225 <assert_contents>
211 <is_valid_xml/> 226 <is_valid_xml/>
212 </assert_contents> 227 </assert_contents>
213 </output> 228 </output>
229 <assert_stdout>
230 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
231 </assert_stdout>
214 </test> 232 </test>
215 <!-- TOPP_FileInfo_7 --> 233 <!-- TOPP_FileInfo_7 -->
216 <test expect_num_outputs="2"> 234 <test expect_num_outputs="2">
217 <section name="adv_opts"> 235 <section name="adv_opts">
218 <param name="force" value="false"/> 236 <param name="force" value="false"/>
219 <param name="test" value="true"/> 237 <param name="test" value="true"/>
220 </section> 238 </section>
221 <param name="in" value="FileInfo_7_input.consensusXML"/> 239 <param name="in" value="FileInfo_7_input.consensusXML"/>
222 <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 240 <output name="out" value="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
223 <param name="m" value="true"/> 241 <param name="m" value="true"/>
224 <param name="p" value="true"/> 242 <param name="p" value="true"/>
225 <param name="s" value="true"/> 243 <param name="s" value="true"/>
226 <param name="d" value="false"/> 244 <param name="d" value="false"/>
227 <param name="c" value="false"/> 245 <param name="c" value="false"/>
231 <output name="ctd_out" ftype="xml"> 249 <output name="ctd_out" ftype="xml">
232 <assert_contents> 250 <assert_contents>
233 <is_valid_xml/> 251 <is_valid_xml/>
234 </assert_contents> 252 </assert_contents>
235 </output> 253 </output>
254 <assert_stdout>
255 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
256 </assert_stdout>
236 </test> 257 </test>
237 <!-- TOPP_FileInfo_9 --> 258 <!-- TOPP_FileInfo_9 -->
238 <test expect_num_outputs="2"> 259 <test expect_num_outputs="2">
239 <section name="adv_opts"> 260 <section name="adv_opts">
240 <param name="force" value="false"/> 261 <param name="force" value="false"/>
241 <param name="test" value="true"/> 262 <param name="test" value="true"/>
242 </section> 263 </section>
243 <param name="in" value="FileInfo_9_input.mzML"/> 264 <param name="in" value="FileInfo_9_input.mzML"/>
244 <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 265 <output name="out" value="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
245 <param name="m" value="true"/> 266 <param name="m" value="true"/>
246 <param name="p" value="true"/> 267 <param name="p" value="true"/>
247 <param name="s" value="true"/> 268 <param name="s" value="true"/>
248 <param name="d" value="false"/> 269 <param name="d" value="false"/>
249 <param name="c" value="false"/> 270 <param name="c" value="false"/>
253 <output name="ctd_out" ftype="xml"> 274 <output name="ctd_out" ftype="xml">
254 <assert_contents> 275 <assert_contents>
255 <is_valid_xml/> 276 <is_valid_xml/>
256 </assert_contents> 277 </assert_contents>
257 </output> 278 </output>
279 <assert_stdout>
280 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
281 </assert_stdout>
258 </test> 282 </test>
259 <!-- TOPP_FileInfo_10 --> 283 <!-- TOPP_FileInfo_10 -->
260 <test expect_num_outputs="2"> 284 <test expect_num_outputs="2">
261 <section name="adv_opts"> 285 <section name="adv_opts">
262 <param name="force" value="false"/> 286 <param name="force" value="false"/>
263 <param name="test" value="true"/> 287 <param name="test" value="true"/>
264 </section> 288 </section>
265 <param name="in" value="FileInfo_10_input.idXML"/> 289 <param name="in" value="FileInfo_10_input.idXML"/>
266 <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 290 <output name="out" value="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
267 <param name="m" value="false"/> 291 <param name="m" value="false"/>
268 <param name="p" value="false"/> 292 <param name="p" value="false"/>
269 <param name="s" value="false"/> 293 <param name="s" value="false"/>
270 <param name="d" value="false"/> 294 <param name="d" value="false"/>
271 <param name="c" value="false"/> 295 <param name="c" value="false"/>
272 <param name="v" value="false"/> 296 <param name="v" value="false"/>
273 <param name="i" value="false"/> 297 <param name="i" value="false"/>
274 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 298 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
275 <output name="ctd_out" ftype="xml"> 299 <output name="ctd_out" ftype="xml">
276 <assert_contents> 300 <assert_contents>
277 <is_valid_xml/> 301 <is_valid_xml/>
278 </assert_contents> 302 </assert_contents>
279 </output> 303 </output>
304 <assert_stdout>
305 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
306 </assert_stdout>
280 </test> 307 </test>
281 <!-- TOPP_FileInfo_12 --> 308 <!-- TOPP_FileInfo_12 -->
282 <test expect_num_outputs="2"> 309 <test expect_num_outputs="2">
283 <section name="adv_opts"> 310 <section name="adv_opts">
284 <param name="force" value="false"/> 311 <param name="force" value="false"/>
296 <output name="ctd_out" ftype="xml"> 323 <output name="ctd_out" ftype="xml">
297 <assert_contents> 324 <assert_contents>
298 <is_valid_xml/> 325 <is_valid_xml/>
299 </assert_contents> 326 </assert_contents>
300 </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>
301 </test> 331 </test>
302 <!-- TOPP_FileInfo_13 --> 332 <!-- TOPP_FileInfo_13 -->
303 <test expect_num_outputs="2"> 333 <test expect_num_outputs="2">
304 <section name="adv_opts"> 334 <section name="adv_opts">
305 <param name="force" value="false"/> 335 <param name="force" value="false"/>
317 <output name="ctd_out" ftype="xml"> 347 <output name="ctd_out" ftype="xml">
318 <assert_contents> 348 <assert_contents>
319 <is_valid_xml/> 349 <is_valid_xml/>
320 </assert_contents> 350 </assert_contents>
321 </output> 351 </output>
352 <assert_stdout>
353 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
354 </assert_stdout>
322 </test> 355 </test>
323 <!-- TOPP_FileInfo_14 --> 356 <!-- TOPP_FileInfo_14 -->
324 <test expect_num_outputs="2"> 357 <test expect_num_outputs="2">
325 <section name="adv_opts"> 358 <section name="adv_opts">
326 <param name="force" value="false"/> 359 <param name="force" value="false"/>
327 <param name="test" value="true"/> 360 <param name="test" value="true"/>
328 </section> 361 </section>
329 <param name="in" value="FileInfo_14_input.mzid"/> 362 <param name="in" value="FileInfo_14_input.mzid"/>
330 <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 363 <output name="out" value="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
331 <param name="m" value="false"/> 364 <param name="m" value="false"/>
332 <param name="p" value="false"/> 365 <param name="p" value="false"/>
333 <param name="s" value="false"/> 366 <param name="s" value="false"/>
334 <param name="d" value="false"/> 367 <param name="d" value="false"/>
335 <param name="c" value="false"/> 368 <param name="c" value="false"/>
339 <output name="ctd_out" ftype="xml"> 372 <output name="ctd_out" ftype="xml">
340 <assert_contents> 373 <assert_contents>
341 <is_valid_xml/> 374 <is_valid_xml/>
342 </assert_contents> 375 </assert_contents>
343 </output> 376 </output>
377 <assert_stdout>
378 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
379 </assert_stdout>
344 </test> 380 </test>
345 <!-- TOPP_FileInfo_15 --> 381 <!-- TOPP_FileInfo_15 -->
346 <test expect_num_outputs="2"> 382 <test expect_num_outputs="2">
347 <section name="adv_opts"> 383 <section name="adv_opts">
348 <param name="force" value="false"/> 384 <param name="force" value="false"/>
349 <param name="test" value="true"/> 385 <param name="test" value="true"/>
350 </section> 386 </section>
351 <param name="in" value="FileInfo_15_input.mzid"/> 387 <param name="in" value="FileInfo_15_input.mzid"/>
352 <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 388 <output name="out" value="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
353 <param name="m" value="false"/> 389 <param name="m" value="false"/>
354 <param name="p" value="false"/> 390 <param name="p" value="false"/>
355 <param name="s" value="false"/> 391 <param name="s" value="false"/>
356 <param name="d" value="false"/> 392 <param name="d" value="false"/>
357 <param name="c" value="false"/> 393 <param name="c" value="false"/>
361 <output name="ctd_out" ftype="xml"> 397 <output name="ctd_out" ftype="xml">
362 <assert_contents> 398 <assert_contents>
363 <is_valid_xml/> 399 <is_valid_xml/>
364 </assert_contents> 400 </assert_contents>
365 </output> 401 </output>
402 <assert_stdout>
403 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
404 </assert_stdout>
366 </test> 405 </test>
367 <!-- TOPP_FileInfo_16 --> 406 <!-- TOPP_FileInfo_16 -->
368 <test expect_num_outputs="2"> 407 <test expect_num_outputs="2">
369 <section name="adv_opts"> 408 <section name="adv_opts">
370 <param name="force" value="false"/> 409 <param name="force" value="false"/>
371 <param name="test" value="true"/> 410 <param name="test" value="true"/>
372 </section> 411 </section>
373 <param name="in" value="FileInfo_16_input.trafoXML"/> 412 <param name="in" value="FileInfo_16_input.trafoXML"/>
374 <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 413 <output name="out" value="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
375 <param name="m" value="false"/> 414 <param name="m" value="false"/>
376 <param name="p" value="false"/> 415 <param name="p" value="false"/>
377 <param name="s" value="false"/> 416 <param name="s" value="false"/>
378 <param name="d" value="false"/> 417 <param name="d" value="false"/>
379 <param name="c" value="false"/> 418 <param name="c" value="false"/>
380 <param name="v" value="false"/> 419 <param name="v" value="false"/>
381 <param name="i" value="false"/> 420 <param name="i" value="false"/>
382 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 421 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
383 <output name="ctd_out" ftype="xml"> 422 <output name="ctd_out" ftype="xml">
384 <assert_contents> 423 <assert_contents>
385 <is_valid_xml/> 424 <is_valid_xml/>
386 </assert_contents> 425 </assert_contents>
387 </output> 426 </output>
427 <assert_stdout>
428 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
429 </assert_stdout>
388 </test> 430 </test>
389 <!-- TOPP_FileInfo_17 --> 431 <!-- TOPP_FileInfo_17 -->
390 <test expect_num_outputs="2"> 432 <test expect_num_outputs="2">
391 <section name="adv_opts"> 433 <section name="adv_opts">
392 <param name="force" value="false"/> 434 <param name="force" value="false"/>
393 <param name="test" value="true"/> 435 <param name="test" value="true"/>
394 </section> 436 </section>
395 <param name="in" value="FileInfo_17_input.fasta"/> 437 <param name="in" value="FileInfo_17_input.fasta"/>
396 <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 438 <output name="out" value="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
397 <param name="m" value="false"/> 439 <param name="m" value="false"/>
398 <param name="p" value="false"/> 440 <param name="p" value="false"/>
399 <param name="s" value="false"/> 441 <param name="s" value="false"/>
400 <param name="d" value="false"/> 442 <param name="d" value="false"/>
401 <param name="c" value="false"/> 443 <param name="c" value="false"/>
402 <param name="v" value="false"/> 444 <param name="v" value="false"/>
403 <param name="i" value="false"/> 445 <param name="i" value="false"/>
404 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 446 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
405 <output name="ctd_out" ftype="xml"> 447 <output name="ctd_out" ftype="xml">
406 <assert_contents> 448 <assert_contents>
407 <is_valid_xml/> 449 <is_valid_xml/>
408 </assert_contents> 450 </assert_contents>
409 </output> 451 </output>
452 <assert_stdout>
453 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
454 </assert_stdout>
410 </test> 455 </test>
411 <!-- TOPP_FileInfo_18 --> 456 <!-- TOPP_FileInfo_18 -->
412 <test expect_num_outputs="2"> 457 <test expect_num_outputs="2">
413 <section name="adv_opts"> 458 <section name="adv_opts">
414 <param name="force" value="false"/> 459 <param name="force" value="false"/>
415 <param name="test" value="true"/> 460 <param name="test" value="true"/>
416 </section> 461 </section>
417 <param name="in" value="FileInfo_18_input.fasta"/> 462 <param name="in" value="FileInfo_18_input.fasta"/>
418 <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> 463 <output name="out" value="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
419 <param name="m" value="false"/> 464 <param name="m" value="false"/>
420 <param name="p" value="false"/> 465 <param name="p" value="false"/>
421 <param name="s" value="false"/> 466 <param name="s" value="false"/>
422 <param name="d" value="false"/> 467 <param name="d" value="false"/>
423 <param name="c" value="false"/> 468 <param name="c" value="false"/>
424 <param name="v" value="false"/> 469 <param name="v" value="false"/>
425 <param name="i" value="false"/> 470 <param name="i" value="false"/>
426 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
427 <output name="ctd_out" ftype="xml"> 472 <output name="ctd_out" ftype="xml">
428 <assert_contents> 473 <assert_contents>
429 <is_valid_xml/> 474 <is_valid_xml/>
430 </assert_contents> 475 </assert_contents>
431 </output> 476 </output>
477 <assert_stdout>
478 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
479 </assert_stdout>
480 </test>
481 <!-- TOPP_FileInfo_19 -->
482 <test expect_num_outputs="2">
483 <section name="adv_opts">
484 <param name="force" value="false"/>
485 <param name="test" value="true"/>
486 </section>
487 <param name="in" value="FAIMS_test_data.mzML"/>
488 <output name="out" value="FileInfo_19_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
489 <param name="m" value="false"/>
490 <param name="p" value="false"/>
491 <param name="s" value="false"/>
492 <param name="d" value="true"/>
493 <param name="c" value="false"/>
494 <param name="v" value="false"/>
495 <param name="i" value="false"/>
496 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
497 <output name="ctd_out" ftype="xml">
498 <assert_contents>
499 <is_valid_xml/>
500 </assert_contents>
501 </output>
502 <assert_stdout>
503 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
504 </assert_stdout>
432 </test> 505 </test>
433 </tests> 506 </tests>
434 <help><![CDATA[Shows basic information about the file, such as data ranges and file type. 507 <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
435 508
436 509
437 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileInfo.html]]></help> 510 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileInfo.html]]></help>
438 <expand macro="references"/> 511 <expand macro="references"/>
439 </tool> 512 </tool>