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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 21:42:42 +0000
parents f82b320ceb90
children
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13:f82b320ceb90 14:fe39f583c19a
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: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> 4 <description>This tool caches the spectra and chromatogram data of an mzML to disk</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> 6 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</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="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> 41 <param argument="-in" type="data" format="mzml,sqmass" label="Input mzML file" help=" select mzml,sqmass 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: that 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: that not all conversion paths work or make sense">
44 <option value="mzML">mzml</option> 43 <option value="mzML">mzml</option>
45 <option value="sqMass">sqmass</option> 44 <option value="sqMass">sqmass</option>
45 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
46 <expand macro="list_string_san" name="out_type"/> 46 <expand macro="list_string_san" name="out_type"/>
47 </param> 47 </param>
48 <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/> 48 <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/>
49 <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/> 49 <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/>
50 <expand macro="adv_opts_macro"> 50 <expand macro="adv_opts_macro">
51 <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> 51 <param argument="-lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
52 <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/> 52 <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
53 <param argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/> 53 <param argument="-lowmem_batchsize" type="integer" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
56 <expand macro="list_string_san" name="test"/> 56 <expand macro="list_string_san" name="test"/>
57 </param> 57 </param>
58 </expand> 58 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </data> 68 </data>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 71 </data>
72 </outputs> 72 </outputs>
73 <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 --> 73 <tests>
74 <!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
74 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
75 <section name="adv_opts"> 76 <section name="adv_opts">
76 <param name="lossy_mass_accuracy" value="-1.0"/> 77 <param name="lossy_mass_accuracy" value="-1.0"/>
77 <param name="process_lowmemory" value="false"/> 78 <param name="process_lowmemory" value="false"/>
78 <param name="lowmem_batchsize" value="500"/> 79 <param name="lowmem_batchsize" value="500"/>
79 <param name="force" value="false"/> 80 <param name="force" value="false"/>
80 <param name="test" value="true"/> 81 <param name="test" value="true"/>
81 </section> 82 </section>
82 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> 83 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
83 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 84 <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
84 <param name="out_type" value="mzML"/> 85 <param name="out_type" value="mzML"/>
85 <param name="lossy_compression" value="true"/> 86 <param name="lossy_compression" value="true"/>
86 <param name="full_meta" value="true"/> 87 <param name="full_meta" value="true"/>
87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 88 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
88 <output name="ctd_out" ftype="xml"> 89 <output name="ctd_out" ftype="xml">
89 <assert_contents> 90 <assert_contents>
90 <is_valid_xml/> 91 <is_valid_xml/>
91 </assert_contents> 92 </assert_contents>
92 </output> 93 </output>
94 <assert_stdout>
95 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
96 </assert_stdout>
93 </test> 97 </test>
94 <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 --> 98 <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 -->
95 <test expect_num_outputs="2"> 99 <test expect_num_outputs="2">
96 <section name="adv_opts"> 100 <section name="adv_opts">
97 <param name="lossy_mass_accuracy" value="-1.0"/> 101 <param name="lossy_mass_accuracy" value="-1.0"/>
99 <param name="lowmem_batchsize" value="500"/> 103 <param name="lowmem_batchsize" value="500"/>
100 <param name="force" value="false"/> 104 <param name="force" value="false"/>
101 <param name="test" value="true"/> 105 <param name="test" value="true"/>
102 </section> 106 </section>
103 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> 107 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
104 <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 108 <output name="out" value="OpenSwathMzMLFileCacher_2_output_1.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
105 <param name="out_type" value="mzML"/> 109 <param name="out_type" value="mzML"/>
106 <param name="lossy_compression" value="true"/> 110 <param name="lossy_compression" value="true"/>
107 <param name="full_meta" value="true"/> 111 <param name="full_meta" value="true"/>
108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
109 <output name="ctd_out" ftype="xml"> 113 <output name="ctd_out" ftype="xml">
110 <assert_contents> 114 <assert_contents>
111 <is_valid_xml/> 115 <is_valid_xml/>
112 </assert_contents> 116 </assert_contents>
113 </output> 117 </output>
118 <assert_stdout>
119 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
120 </assert_stdout>
114 </test> 121 </test>
115 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 --> 122 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 -->
116 <test expect_num_outputs="2"> 123 <test expect_num_outputs="2">
117 <section name="adv_opts"> 124 <section name="adv_opts">
118 <param name="lossy_mass_accuracy" value="0.0001"/> 125 <param name="lossy_mass_accuracy" value="0.0001"/>
120 <param name="lowmem_batchsize" value="500"/> 127 <param name="lowmem_batchsize" value="500"/>
121 <param name="force" value="false"/> 128 <param name="force" value="false"/>
122 <param name="test" value="true"/> 129 <param name="test" value="true"/>
123 </section> 130 </section>
124 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> 131 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
125 <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> 132 <output name="out" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
126 <param name="out_type" value="sqMass"/> 133 <param name="out_type" value="sqMass"/>
127 <param name="lossy_compression" value="true"/> 134 <param name="lossy_compression" value="true"/>
128 <param name="full_meta" value="true"/> 135 <param name="full_meta" value="true"/>
129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 136 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
130 <output name="ctd_out" ftype="xml"> 137 <output name="ctd_out" ftype="xml">
131 <assert_contents> 138 <assert_contents>
132 <is_valid_xml/> 139 <is_valid_xml/>
133 </assert_contents> 140 </assert_contents>
134 </output> 141 </output>
142 <assert_stdout>
143 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
144 </assert_stdout>
135 </test> 145 </test>
136 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 --> 146 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 -->
137 <test expect_num_outputs="2"> 147 <test expect_num_outputs="2">
138 <section name="adv_opts"> 148 <section name="adv_opts">
139 <param name="lossy_mass_accuracy" value="-1.0"/> 149 <param name="lossy_mass_accuracy" value="-1.0"/>
141 <param name="lowmem_batchsize" value="500"/> 151 <param name="lowmem_batchsize" value="500"/>
142 <param name="force" value="false"/> 152 <param name="force" value="false"/>
143 <param name="test" value="true"/> 153 <param name="test" value="true"/>
144 </section> 154 </section>
145 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> 155 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
146 <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 156 <output name="out" value="OpenSwathMzMLFileCacher_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
147 <param name="out_type" value="mzML"/> 157 <param name="out_type" value="mzML"/>
148 <param name="lossy_compression" value="true"/> 158 <param name="lossy_compression" value="true"/>
149 <param name="full_meta" value="true"/> 159 <param name="full_meta" value="true"/>
150 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
151 <output name="ctd_out" ftype="xml"> 161 <output name="ctd_out" ftype="xml">
152 <assert_contents> 162 <assert_contents>
153 <is_valid_xml/> 163 <is_valid_xml/>
154 </assert_contents> 164 </assert_contents>
155 </output> 165 </output>
166 <assert_stdout>
167 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
168 </assert_stdout>
156 </test> 169 </test>
157 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 --> 170 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 -->
158 <test expect_num_outputs="2"> 171 <test expect_num_outputs="2">
159 <section name="adv_opts"> 172 <section name="adv_opts">
160 <param name="lossy_mass_accuracy" value="-1.0"/> 173 <param name="lossy_mass_accuracy" value="-1.0"/>
162 <param name="lowmem_batchsize" value="500"/> 175 <param name="lowmem_batchsize" value="500"/>
163 <param name="force" value="false"/> 176 <param name="force" value="false"/>
164 <param name="test" value="true"/> 177 <param name="test" value="true"/>
165 </section> 178 </section>
166 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> 179 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
167 <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> 180 <output name="out" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
168 <param name="out_type" value="sqMass"/> 181 <param name="out_type" value="sqMass"/>
169 <param name="lossy_compression" value="true"/> 182 <param name="lossy_compression" value="true"/>
170 <param name="full_meta" value="true"/> 183 <param name="full_meta" value="true"/>
171 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
172 <output name="ctd_out" ftype="xml"> 185 <output name="ctd_out" ftype="xml">
173 <assert_contents> 186 <assert_contents>
174 <is_valid_xml/> 187 <is_valid_xml/>
175 </assert_contents> 188 </assert_contents>
176 </output> 189 </output>
190 <assert_stdout>
191 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
192 </assert_stdout>
177 </test> 193 </test>
178 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 --> 194 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 -->
179 <test expect_num_outputs="2"> 195 <test expect_num_outputs="2">
180 <section name="adv_opts"> 196 <section name="adv_opts">
181 <param name="lossy_mass_accuracy" value="-1.0"/> 197 <param name="lossy_mass_accuracy" value="-1.0"/>
183 <param name="lowmem_batchsize" value="500"/> 199 <param name="lowmem_batchsize" value="500"/>
184 <param name="force" value="false"/> 200 <param name="force" value="false"/>
185 <param name="test" value="true"/> 201 <param name="test" value="true"/>
186 </section> 202 </section>
187 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> 203 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
188 <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 204 <output name="out" value="OpenSwathMzMLFileCacher_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
189 <param name="out_type" value="mzML"/> 205 <param name="out_type" value="mzML"/>
190 <param name="lossy_compression" value="true"/> 206 <param name="lossy_compression" value="true"/>
191 <param name="full_meta" value="true"/> 207 <param name="full_meta" value="true"/>
192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
193 <output name="ctd_out" ftype="xml"> 209 <output name="ctd_out" ftype="xml">
194 <assert_contents> 210 <assert_contents>
195 <is_valid_xml/> 211 <is_valid_xml/>
196 </assert_contents> 212 </assert_contents>
197 </output> 213 </output>
214 <assert_stdout>
215 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
216 </assert_stdout>
198 </test> 217 </test>
199 <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 --> 218 <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 -->
200 <test expect_num_outputs="2"> 219 <test expect_num_outputs="2">
201 <section name="adv_opts"> 220 <section name="adv_opts">
202 <param name="lossy_mass_accuracy" value="-1.0"/> 221 <param name="lossy_mass_accuracy" value="-1.0"/>
204 <param name="lowmem_batchsize" value="500"/> 223 <param name="lowmem_batchsize" value="500"/>
205 <param name="force" value="false"/> 224 <param name="force" value="false"/>
206 <param name="test" value="true"/> 225 <param name="test" value="true"/>
207 </section> 226 </section>
208 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> 227 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
209 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 228 <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
210 <param name="out_type" value="mzML"/> 229 <param name="out_type" value="mzML"/>
211 <param name="lossy_compression" value="true"/> 230 <param name="lossy_compression" value="true"/>
212 <param name="full_meta" value="true"/> 231 <param name="full_meta" value="true"/>
213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
214 <output name="ctd_out" ftype="xml"> 233 <output name="ctd_out" ftype="xml">
215 <assert_contents> 234 <assert_contents>
216 <is_valid_xml/> 235 <is_valid_xml/>
217 </assert_contents> 236 </assert_contents>
218 </output> 237 </output>
238 <assert_stdout>
239 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
240 </assert_stdout>
241 </test>
242 <!-- TOPP_OpenSwathAnalyzer_test_3_prepare -->
243 <test expect_num_outputs="2">
244 <section name="adv_opts">
245 <param name="lossy_mass_accuracy" value="-1.0"/>
246 <param name="process_lowmemory" value="false"/>
247 <param name="lowmem_batchsize" value="500"/>
248 <param name="force" value="false"/>
249 <param name="test" value="true"/>
250 </section>
251 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
252 <output name="out" value="OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
253 <param name="out_type" value="mzML"/>
254 <param name="lossy_compression" value="true"/>
255 <param name="full_meta" value="true"/>
256 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
257 <output name="ctd_out" ftype="xml">
258 <assert_contents>
259 <is_valid_xml/>
260 </assert_contents>
261 </output>
262 <assert_stdout>
263 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
264 </assert_stdout>
219 </test> 265 </test>
220 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 --> 266 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 -->
221 <test expect_num_outputs="2"> 267 <test expect_num_outputs="2">
222 <section name="adv_opts"> 268 <section name="adv_opts">
223 <param name="lossy_mass_accuracy" value="-1.0"/> 269 <param name="lossy_mass_accuracy" value="-1.0"/>
225 <param name="lowmem_batchsize" value="500"/> 271 <param name="lowmem_batchsize" value="500"/>
226 <param name="force" value="false"/> 272 <param name="force" value="false"/>
227 <param name="test" value="true"/> 273 <param name="test" value="true"/>
228 </section> 274 </section>
229 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> 275 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
230 <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> 276 <output name="out" value="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
231 <param name="out_type" value="mzML"/> 277 <param name="out_type" value="mzML"/>
232 <param name="lossy_compression" value="true"/> 278 <param name="lossy_compression" value="true"/>
233 <param name="full_meta" value="true"/> 279 <param name="full_meta" value="true"/>
234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 280 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
235 <output name="ctd_out" ftype="xml"> 281 <output name="ctd_out" ftype="xml">
236 <assert_contents> 282 <assert_contents>
237 <is_valid_xml/> 283 <is_valid_xml/>
238 </assert_contents> 284 </assert_contents>
239 </output> 285 </output>
286 <assert_stdout>
287 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
288 </assert_stdout>
240 </test> 289 </test>
241 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 --> 290 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 -->
242 <test expect_num_outputs="2"> 291 <test expect_num_outputs="2">
243 <section name="adv_opts"> 292 <section name="adv_opts">
244 <param name="lossy_mass_accuracy" value="-1.0"/> 293 <param name="lossy_mass_accuracy" value="-1.0"/>
246 <param name="lowmem_batchsize" value="500"/> 295 <param name="lowmem_batchsize" value="500"/>
247 <param name="force" value="false"/> 296 <param name="force" value="false"/>
248 <param name="test" value="true"/> 297 <param name="test" value="true"/>
249 </section> 298 </section>
250 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> 299 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
251 <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> 300 <output name="out" value="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
252 <param name="out_type" value="mzML"/> 301 <param name="out_type" value="mzML"/>
253 <param name="lossy_compression" value="true"/> 302 <param name="lossy_compression" value="true"/>
254 <param name="full_meta" value="true"/> 303 <param name="full_meta" value="true"/>
255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
256 <output name="ctd_out" ftype="xml"> 305 <output name="ctd_out" ftype="xml">
257 <assert_contents> 306 <assert_contents>
258 <is_valid_xml/> 307 <is_valid_xml/>
259 </assert_contents> 308 </assert_contents>
260 </output> 309 </output>
310 <assert_stdout>
311 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
312 </assert_stdout>
261 </test> 313 </test>
262 <!-- TOPP_OpenSwathWorkflow_14_step2 --> 314 <!-- TOPP_OpenSwathWorkflow_14_step2 -->
263 <test expect_num_outputs="2"> 315 <test expect_num_outputs="2">
264 <section name="adv_opts"> 316 <section name="adv_opts">
265 <param name="lossy_mass_accuracy" value="0.0001"/> 317 <param name="lossy_mass_accuracy" value="0.0001"/>
267 <param name="lowmem_batchsize" value="500"/> 319 <param name="lowmem_batchsize" value="500"/>
268 <param name="force" value="false"/> 320 <param name="force" value="false"/>
269 <param name="test" value="true"/> 321 <param name="test" value="true"/>
270 </section> 322 </section>
271 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> 323 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
272 <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 324 <output name="out" value="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
273 <param name="out_type" value="mzML"/> 325 <param name="out_type" value="mzML"/>
274 <param name="lossy_compression" value="false"/> 326 <param name="lossy_compression" value="false"/>
275 <param name="full_meta" value="false"/> 327 <param name="full_meta" value="false"/>
276 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
277 <output name="ctd_out" ftype="xml"> 329 <output name="ctd_out" ftype="xml">
278 <assert_contents> 330 <assert_contents>
279 <is_valid_xml/> 331 <is_valid_xml/>
280 </assert_contents> 332 </assert_contents>
281 </output> 333 </output>
334 <assert_stdout>
335 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
336 </assert_stdout>
337 </test>
338 <!-- TOPP_OpenSwathWorkflow_16_prepare -->
339 <test expect_num_outputs="2">
340 <section name="adv_opts">
341 <param name="lossy_mass_accuracy" value="0.0001"/>
342 <param name="process_lowmemory" value="false"/>
343 <param name="lowmem_batchsize" value="500"/>
344 <param name="force" value="false"/>
345 <param name="test" value="true"/>
346 </section>
347 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
348 <output name="out" value="OpenSwathWorkflow_16_input.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
349 <param name="out_type" value="sqMass"/>
350 <param name="lossy_compression" value="true"/>
351 <param name="full_meta" value="true"/>
352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
353 <output name="ctd_out" ftype="xml">
354 <assert_contents>
355 <is_valid_xml/>
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>
282 </test> 361 </test>
283 </tests> 362 </tests>
284 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. 363 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk.
285 364
286 365
287 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> 366 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathMzMLFileCacher.html]]></help>
288 <expand macro="references"/> 367 <expand macro="references"/>
289 </tool> 368 </tool>