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comparison OpenSwathMzMLFileCacher.xml @ 13:f82b320ceb90 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:04:12 +0000
parents fc775d5aa321
children
comparison
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12:f9ed7e074900 13:f82b320ceb90
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>