Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher
comparison OpenSwathMzMLFileCacher.xml @ 13:f82b320ceb90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:04:12 +0000 |
parents | fc775d5aa321 |
children | fe39f583c19a |
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12:f9ed7e074900 | 13:f82b320ceb90 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Targeted Experiments]--> | 3 <!--Proposed Tool Section: [Targeted Experiments]--> |
4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <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> | 5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> | 7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
39 <configfiles> | 37 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 38 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 40 </configfiles> |
43 <inputs> | 41 <inputs> |
44 <param name="in" argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> | 42 <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> |
45 <param name="out_type" 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"> | 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"> |
46 <option value="mzML">mzml</option> | 44 <option value="mzML">mzml</option> |
47 <option value="sqMass">sqmass</option> | 45 <option value="sqMass">sqmass</option> |
48 <expand macro="list_string_san"/> | 46 <expand macro="list_string_san" name="out_type"/> |
49 </param> | 47 </param> |
50 <param name="lossy_compression" 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=""/> |
51 <param name="full_meta" 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=""/> |
52 <expand macro="adv_opts_macro"> | 50 <expand macro="adv_opts_macro"> |
53 <param name="lossy_mass_accuracy" 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" 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)"/> |
54 <param name="process_lowmemory" 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"/> |
55 <param name="lowmem_batchsize" 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" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/> |
56 <param name="force" 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=""/> |
57 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
58 <expand macro="list_string_san"/> | 56 <expand macro="list_string_san" name="test"/> |
59 </param> | 57 </param> |
60 </expand> | 58 </expand> |
61 <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"> |
62 <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> |
63 </param> | 61 </param> |
64 </inputs> | 62 </inputs> |
65 <outputs> | 63 <outputs> |
66 <data name="out" label="${tool.name} on ${on_string}: out"> | 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"> |
67 <change_format> | 65 <change_format> |
68 <when input="out_type" value="mzML" format="mzml"/> | |
69 <when input="out_type" value="sqMass" format="sqmass"/> | 66 <when input="out_type" value="sqMass" format="sqmass"/> |
70 </change_format> | 67 </change_format> |
71 </data> | 68 </data> |
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
73 <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> |
74 </data> | 71 </data> |
75 </outputs> | 72 </outputs> |
76 <tests> | 73 <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 --> |
77 <expand macro="autotest_OpenSwathMzMLFileCacher"/> | 74 <test expect_num_outputs="2"> |
78 <expand macro="manutest_OpenSwathMzMLFileCacher"/> | 75 <section name="adv_opts"> |
76 <param name="lossy_mass_accuracy" value="-1.0"/> | |
77 <param name="process_lowmemory" value="false"/> | |
78 <param name="lowmem_batchsize" value="500"/> | |
79 <param name="force" value="false"/> | |
80 <param name="test" value="true"/> | |
81 </section> | |
82 <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 <param name="out_type" value="mzML"/> | |
85 <param name="lossy_compression" value="true"/> | |
86 <param name="full_meta" value="true"/> | |
87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
88 <output name="ctd_out" ftype="xml"> | |
89 <assert_contents> | |
90 <is_valid_xml/> | |
91 </assert_contents> | |
92 </output> | |
93 </test> | |
94 <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 --> | |
95 <test expect_num_outputs="2"> | |
96 <section name="adv_opts"> | |
97 <param name="lossy_mass_accuracy" value="-1.0"/> | |
98 <param name="process_lowmemory" value="false"/> | |
99 <param name="lowmem_batchsize" value="500"/> | |
100 <param name="force" value="false"/> | |
101 <param name="test" value="true"/> | |
102 </section> | |
103 <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"/> | |
105 <param name="out_type" value="mzML"/> | |
106 <param name="lossy_compression" value="true"/> | |
107 <param name="full_meta" value="true"/> | |
108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
109 <output name="ctd_out" ftype="xml"> | |
110 <assert_contents> | |
111 <is_valid_xml/> | |
112 </assert_contents> | |
113 </output> | |
114 </test> | |
115 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 --> | |
116 <test expect_num_outputs="2"> | |
117 <section name="adv_opts"> | |
118 <param name="lossy_mass_accuracy" value="0.0001"/> | |
119 <param name="process_lowmemory" value="false"/> | |
120 <param name="lowmem_batchsize" value="500"/> | |
121 <param name="force" value="false"/> | |
122 <param name="test" value="true"/> | |
123 </section> | |
124 <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"/> | |
126 <param name="out_type" value="sqMass"/> | |
127 <param name="lossy_compression" value="true"/> | |
128 <param name="full_meta" value="true"/> | |
129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
130 <output name="ctd_out" ftype="xml"> | |
131 <assert_contents> | |
132 <is_valid_xml/> | |
133 </assert_contents> | |
134 </output> | |
135 </test> | |
136 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 --> | |
137 <test expect_num_outputs="2"> | |
138 <section name="adv_opts"> | |
139 <param name="lossy_mass_accuracy" value="-1.0"/> | |
140 <param name="process_lowmemory" value="false"/> | |
141 <param name="lowmem_batchsize" value="500"/> | |
142 <param name="force" value="false"/> | |
143 <param name="test" value="true"/> | |
144 </section> | |
145 <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"/> | |
147 <param name="out_type" value="mzML"/> | |
148 <param name="lossy_compression" value="true"/> | |
149 <param name="full_meta" value="true"/> | |
150 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
151 <output name="ctd_out" ftype="xml"> | |
152 <assert_contents> | |
153 <is_valid_xml/> | |
154 </assert_contents> | |
155 </output> | |
156 </test> | |
157 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 --> | |
158 <test expect_num_outputs="2"> | |
159 <section name="adv_opts"> | |
160 <param name="lossy_mass_accuracy" value="-1.0"/> | |
161 <param name="process_lowmemory" value="false"/> | |
162 <param name="lowmem_batchsize" value="500"/> | |
163 <param name="force" value="false"/> | |
164 <param name="test" value="true"/> | |
165 </section> | |
166 <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"/> | |
168 <param name="out_type" value="sqMass"/> | |
169 <param name="lossy_compression" value="true"/> | |
170 <param name="full_meta" value="true"/> | |
171 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
172 <output name="ctd_out" ftype="xml"> | |
173 <assert_contents> | |
174 <is_valid_xml/> | |
175 </assert_contents> | |
176 </output> | |
177 </test> | |
178 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 --> | |
179 <test expect_num_outputs="2"> | |
180 <section name="adv_opts"> | |
181 <param name="lossy_mass_accuracy" value="-1.0"/> | |
182 <param name="process_lowmemory" value="false"/> | |
183 <param name="lowmem_batchsize" value="500"/> | |
184 <param name="force" value="false"/> | |
185 <param name="test" value="true"/> | |
186 </section> | |
187 <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"/> | |
189 <param name="out_type" value="mzML"/> | |
190 <param name="lossy_compression" value="true"/> | |
191 <param name="full_meta" value="true"/> | |
192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
193 <output name="ctd_out" ftype="xml"> | |
194 <assert_contents> | |
195 <is_valid_xml/> | |
196 </assert_contents> | |
197 </output> | |
198 </test> | |
199 <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 --> | |
200 <test expect_num_outputs="2"> | |
201 <section name="adv_opts"> | |
202 <param name="lossy_mass_accuracy" value="-1.0"/> | |
203 <param name="process_lowmemory" value="true"/> | |
204 <param name="lowmem_batchsize" value="500"/> | |
205 <param name="force" value="false"/> | |
206 <param name="test" value="true"/> | |
207 </section> | |
208 <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"/> | |
210 <param name="out_type" value="mzML"/> | |
211 <param name="lossy_compression" value="true"/> | |
212 <param name="full_meta" value="true"/> | |
213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
214 <output name="ctd_out" ftype="xml"> | |
215 <assert_contents> | |
216 <is_valid_xml/> | |
217 </assert_contents> | |
218 </output> | |
219 </test> | |
220 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 --> | |
221 <test expect_num_outputs="2"> | |
222 <section name="adv_opts"> | |
223 <param name="lossy_mass_accuracy" value="-1.0"/> | |
224 <param name="process_lowmemory" value="false"/> | |
225 <param name="lowmem_batchsize" value="500"/> | |
226 <param name="force" value="false"/> | |
227 <param name="test" value="true"/> | |
228 </section> | |
229 <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"/> | |
231 <param name="out_type" value="mzML"/> | |
232 <param name="lossy_compression" value="true"/> | |
233 <param name="full_meta" value="true"/> | |
234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
235 <output name="ctd_out" ftype="xml"> | |
236 <assert_contents> | |
237 <is_valid_xml/> | |
238 </assert_contents> | |
239 </output> | |
240 </test> | |
241 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 --> | |
242 <test expect_num_outputs="2"> | |
243 <section name="adv_opts"> | |
244 <param name="lossy_mass_accuracy" value="-1.0"/> | |
245 <param name="process_lowmemory" value="false"/> | |
246 <param name="lowmem_batchsize" value="500"/> | |
247 <param name="force" value="false"/> | |
248 <param name="test" value="true"/> | |
249 </section> | |
250 <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"/> | |
252 <param name="out_type" value="mzML"/> | |
253 <param name="lossy_compression" value="true"/> | |
254 <param name="full_meta" value="true"/> | |
255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
256 <output name="ctd_out" ftype="xml"> | |
257 <assert_contents> | |
258 <is_valid_xml/> | |
259 </assert_contents> | |
260 </output> | |
261 </test> | |
262 <!-- TOPP_OpenSwathWorkflow_14_step2 --> | |
263 <test expect_num_outputs="2"> | |
264 <section name="adv_opts"> | |
265 <param name="lossy_mass_accuracy" value="0.0001"/> | |
266 <param name="process_lowmemory" value="false"/> | |
267 <param name="lowmem_batchsize" value="500"/> | |
268 <param name="force" value="false"/> | |
269 <param name="test" value="true"/> | |
270 </section> | |
271 <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"/> | |
273 <param name="out_type" value="mzML"/> | |
274 <param name="lossy_compression" value="false"/> | |
275 <param name="full_meta" value="false"/> | |
276 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
277 <output name="ctd_out" ftype="xml"> | |
278 <assert_contents> | |
279 <is_valid_xml/> | |
280 </assert_contents> | |
281 </output> | |
282 </test> | |
79 </tests> | 283 </tests> |
80 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. | 284 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. |
81 | 285 |
82 | 286 |
83 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> | 287 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> |
84 <expand macro="references"/> | 288 <expand macro="references"/> |
85 </tool> | 289 </tool> |