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comparison FileConverter.xml @ 15:2a93a25f0599 draft

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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 19:09:16 +0000
parents 62e19948b50f
children 8b6336c903ef
comparison
equal deleted inserted replaced
14:9b7977080f6d 15:2a93a25f0599
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converts between different MS file formats.</description> 5 <description>Converts between different MS file formats.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileConverter</token> 7 <token name="@EXECUTABLE@">FileConverter</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[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "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="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw data sets(s)"/> 42 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw data sets(s)"/>
45 <param name="out_type" argument="-out_type" 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" 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="consensusXML">consensusxml</option> 44 <option value="consensusXML">consensusxml</option>
47 <option value="csv">csv</option> 45 <option value="csv">csv</option>
48 <option value="dta2d">dta2d</option> 46 <option value="dta2d">dta2d</option>
49 <option value="edta">edta</option> 47 <option value="edta">edta</option>
50 <option value="featureXML">featurexml</option> 48 <option value="featureXML">featurexml</option>
51 <option value="mgf">mgf</option> 49 <option value="mgf">mgf</option>
52 <option value="mzData">mzdata</option> 50 <option value="mzData">mzdata</option>
53 <option value="mzML">mzml</option> 51 <option value="mzML">mzml</option>
54 <option value="mzXML">mzxml</option> 52 <option value="mzXML">mzxml</option>
55 <expand macro="list_string_san"/> 53 <option value="oms">sqlite (oms)</option>
54 <expand macro="list_string_san" name="out_type"/>
56 </param> 55 </param>
57 <expand macro="adv_opts_macro"> 56 <expand macro="adv_opts_macro">
58 <param name="UID_postprocessing" argument="-UID_postprocessing" display="radio" type="select" optional="false" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs"> 57 <param argument="-UID_postprocessing" type="select" optional="true" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
59 <option value="none">none</option> 58 <option value="none">none</option>
60 <option value="ensure" selected="true">ensure</option> 59 <option value="ensure" selected="true">ensure</option>
61 <option value="reassign">reassign</option> 60 <option value="reassign">reassign</option>
62 <expand macro="list_string_san"/> 61 <expand macro="list_string_san" name="UID_postprocessing"/>
63 </param> 62 </param>
64 <param name="TIC_DTA2D" argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/> 63 <param argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/>
65 <param name="MGF_compact" argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/> 64 <param argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/>
66 <param name="force_MaxQuant_compatibility" argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/> 65 <param argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
67 <param name="convert_to_chromatograms" argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/> 66 <param argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
68 <param name="force_TPP_compatibility" argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/> 67 <param argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
69 <param name="change_im_format" argument="-change_im_format" display="radio" type="select" optional="false" label="[mzML output only] How to store ion mobility scans (none: no change in format, multiple: store each frame as multiple scans, one per drift time value, single: store whole frame as single scan with IM values in a FloatDataArray" help=""> 68 <param argument="-change_im_format" type="select" optional="true" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
70 <option value="none" selected="true">none</option> 69 <option value="none" selected="true">none</option>
71 <option value="multiple">multiple</option> 70 <option value="concatenated">concatenated</option>
72 <option value="single">single</option> 71 <option value="multiple_spectra">multiple_spectra</option>
73 <expand macro="list_string_san"/> 72 <option value="mixed">mixed</option>
73 <expand macro="list_string_san" name="change_im_format"/>
74 </param> 74 </param>
75 <param name="write_scan_index" argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/> 75 <param argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
76 <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/> 76 <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
77 <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)"/> 77 <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)"/>
78 <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"/> 78 <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"/>
79 <param name="no_peak_picking" argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/> 79 <param argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
82 <expand macro="list_string_san"/> 82 <expand macro="list_string_san" name="test"/>
83 </param> 83 </param>
84 </expand> 84 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param> 87 </param>
88 </inputs> 88 </inputs>
89 <outputs> 89 <outputs>
90 <data name="out" label="${tool.name} on ${on_string}: out"> 90 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
91 <change_format> 91 <change_format>
92 <when input="out_type" value="consensusXML" format="consensusxml"/>
93 <when input="out_type" value="csv" format="csv"/> 92 <when input="out_type" value="csv" format="csv"/>
94 <when input="out_type" value="dta2d" format="dta2d"/> 93 <when input="out_type" value="dta2d" format="dta2d"/>
95 <when input="out_type" value="edta" format="edta"/> 94 <when input="out_type" value="edta" format="edta"/>
96 <when input="out_type" value="featureXML" format="featurexml"/> 95 <when input="out_type" value="featureXML" format="featurexml"/>
97 <when input="out_type" value="mgf" format="mgf"/> 96 <when input="out_type" value="mgf" format="mgf"/>
98 <when input="out_type" value="mzData" format="mzdata"/> 97 <when input="out_type" value="mzData" format="mzdata"/>
99 <when input="out_type" value="mzML" format="mzml"/> 98 <when input="out_type" value="mzML" format="mzml"/>
100 <when input="out_type" value="mzXML" format="mzxml"/> 99 <when input="out_type" value="mzXML" format="mzxml"/>
100 <when input="out_type" value="oms" format="sqlite"/>
101 </change_format> 101 </change_format>
102 </data> 102 </data>
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
105 </data> 105 </data>
106 </outputs> 106 </outputs>
107 <tests> 107 <tests><!-- TOPP_FileConverter_1 -->
108 <expand macro="autotest_FileConverter"/> 108 <test expect_num_outputs="2">
109 <expand macro="manutest_FileConverter"/> 109 <section name="adv_opts">
110 </tests> 110 <param name="UID_postprocessing" value="ensure"/>
111 <param name="TIC_DTA2D" value="false"/>
112 <param name="MGF_compact" value="false"/>
113 <param name="force_MaxQuant_compatibility" value="false"/>
114 <param name="force_TPP_compatibility" value="false"/>
115 <param name="convert_to_chromatograms" value="false"/>
116 <param name="change_im_format" value="none"/>
117 <param name="write_scan_index" value="true"/>
118 <param name="lossy_compression" value="false"/>
119 <param name="lossy_mass_accuracy" value="-1.0"/>
120 <param name="process_lowmemory" value="false"/>
121 <param name="no_peak_picking" value="false"/>
122 <param name="force" value="false"/>
123 <param name="test" value="true"/>
124 </section>
125 <param name="in" value="FileConverter_1_input.mzData"/>
126 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
127 <param name="out_type" value="mzML"/>
128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
129 <output name="ctd_out" ftype="xml">
130 <assert_contents>
131 <is_valid_xml/>
132 </assert_contents>
133 </output>
134 </test>
135 <!-- TOPP_FileConverter_2 -->
136 <test expect_num_outputs="2">
137 <section name="adv_opts">
138 <param name="UID_postprocessing" value="ensure"/>
139 <param name="TIC_DTA2D" value="false"/>
140 <param name="MGF_compact" value="false"/>
141 <param name="force_MaxQuant_compatibility" value="false"/>
142 <param name="force_TPP_compatibility" value="false"/>
143 <param name="convert_to_chromatograms" value="false"/>
144 <param name="change_im_format" value="none"/>
145 <param name="write_scan_index" value="true"/>
146 <param name="lossy_compression" value="false"/>
147 <param name="lossy_mass_accuracy" value="-1.0"/>
148 <param name="process_lowmemory" value="false"/>
149 <param name="no_peak_picking" value="false"/>
150 <param name="force" value="false"/>
151 <param name="test" value="true"/>
152 </section>
153 <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
154 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
155 <param name="out_type" value="mzML"/>
156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
157 <output name="ctd_out" ftype="xml">
158 <assert_contents>
159 <is_valid_xml/>
160 </assert_contents>
161 </output>
162 </test>
163 <!-- TOPP_FileConverter_3 -->
164 <test expect_num_outputs="2">
165 <section name="adv_opts">
166 <param name="UID_postprocessing" value="ensure"/>
167 <param name="TIC_DTA2D" value="false"/>
168 <param name="MGF_compact" value="false"/>
169 <param name="force_MaxQuant_compatibility" value="false"/>
170 <param name="force_TPP_compatibility" value="false"/>
171 <param name="convert_to_chromatograms" value="false"/>
172 <param name="change_im_format" value="none"/>
173 <param name="write_scan_index" value="true"/>
174 <param name="lossy_compression" value="false"/>
175 <param name="lossy_mass_accuracy" value="-1.0"/>
176 <param name="process_lowmemory" value="false"/>
177 <param name="no_peak_picking" value="false"/>
178 <param name="force" value="false"/>
179 <param name="test" value="true"/>
180 </section>
181 <param name="in" value="FileConverter_3_input.featureXML"/>
182 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
183 <param name="out_type" value="mzML"/>
184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
185 <output name="ctd_out" ftype="xml">
186 <assert_contents>
187 <is_valid_xml/>
188 </assert_contents>
189 </output>
190 </test>
191 <!-- TOPP_FileConverter_4 -->
192 <test expect_num_outputs="2">
193 <section name="adv_opts">
194 <param name="UID_postprocessing" value="ensure"/>
195 <param name="TIC_DTA2D" value="false"/>
196 <param name="MGF_compact" value="false"/>
197 <param name="force_MaxQuant_compatibility" value="false"/>
198 <param name="force_TPP_compatibility" value="false"/>
199 <param name="convert_to_chromatograms" value="false"/>
200 <param name="change_im_format" value="none"/>
201 <param name="write_scan_index" value="true"/>
202 <param name="lossy_compression" value="false"/>
203 <param name="lossy_mass_accuracy" value="-1.0"/>
204 <param name="process_lowmemory" value="false"/>
205 <param name="no_peak_picking" value="false"/>
206 <param name="force" value="false"/>
207 <param name="test" value="true"/>
208 </section>
209 <param name="in" value="FileConverter_4_input.mzXML"/>
210 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
211 <param name="out_type" value="mzML"/>
212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
213 <output name="ctd_out" ftype="xml">
214 <assert_contents>
215 <is_valid_xml/>
216 </assert_contents>
217 </output>
218 </test>
219 <!-- TOPP_FileConverter_5 -->
220 <test expect_num_outputs="2">
221 <section name="adv_opts">
222 <param name="UID_postprocessing" value="ensure"/>
223 <param name="TIC_DTA2D" value="false"/>
224 <param name="MGF_compact" value="false"/>
225 <param name="force_MaxQuant_compatibility" value="false"/>
226 <param name="force_TPP_compatibility" value="false"/>
227 <param name="convert_to_chromatograms" value="false"/>
228 <param name="change_im_format" value="none"/>
229 <param name="write_scan_index" value="true"/>
230 <param name="lossy_compression" value="false"/>
231 <param name="lossy_mass_accuracy" value="-1.0"/>
232 <param name="process_lowmemory" value="false"/>
233 <param name="no_peak_picking" value="false"/>
234 <param name="force" value="false"/>
235 <param name="test" value="true"/>
236 </section>
237 <param name="in" value="FileConverter_5_input.mzML"/>
238 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
239 <param name="out_type" value="mzXML"/>
240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
241 <output name="ctd_out" ftype="xml">
242 <assert_contents>
243 <is_valid_xml/>
244 </assert_contents>
245 </output>
246 </test>
247 <!-- TOPP_FileConverter_6 -->
248 <test expect_num_outputs="2">
249 <section name="adv_opts">
250 <param name="UID_postprocessing" value="ensure"/>
251 <param name="TIC_DTA2D" value="false"/>
252 <param name="MGF_compact" value="false"/>
253 <param name="force_MaxQuant_compatibility" value="false"/>
254 <param name="force_TPP_compatibility" value="false"/>
255 <param name="convert_to_chromatograms" value="false"/>
256 <param name="change_im_format" value="none"/>
257 <param name="write_scan_index" value="true"/>
258 <param name="lossy_compression" value="false"/>
259 <param name="lossy_mass_accuracy" value="-1.0"/>
260 <param name="process_lowmemory" value="false"/>
261 <param name="no_peak_picking" value="false"/>
262 <param name="force" value="false"/>
263 <param name="test" value="true"/>
264 </section>
265 <param name="in" value="FileConverter_6_input.mzML"/>
266 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
267 <param name="out_type" value="mzXML"/>
268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
269 <output name="ctd_out" ftype="xml">
270 <assert_contents>
271 <is_valid_xml/>
272 </assert_contents>
273 </output>
274 </test>
275 <!-- TOPP_FileConverter_7 -->
276 <test expect_num_outputs="2">
277 <section name="adv_opts">
278 <param name="UID_postprocessing" value="ensure"/>
279 <param name="TIC_DTA2D" value="false"/>
280 <param name="MGF_compact" value="false"/>
281 <param name="force_MaxQuant_compatibility" value="false"/>
282 <param name="force_TPP_compatibility" value="false"/>
283 <param name="convert_to_chromatograms" value="false"/>
284 <param name="change_im_format" value="none"/>
285 <param name="write_scan_index" value="true"/>
286 <param name="lossy_compression" value="false"/>
287 <param name="lossy_mass_accuracy" value="-1.0"/>
288 <param name="process_lowmemory" value="false"/>
289 <param name="no_peak_picking" value="false"/>
290 <param name="force" value="false"/>
291 <param name="test" value="true"/>
292 </section>
293 <param name="in" value="FileConverter_7_input.consensusXML"/>
294 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
295 <param name="out_type" value="featureXML"/>
296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
297 <output name="ctd_out" ftype="xml">
298 <assert_contents>
299 <is_valid_xml/>
300 </assert_contents>
301 </output>
302 </test>
303 <!-- TOPP_FileConverter_8 -->
304 <test expect_num_outputs="2">
305 <section name="adv_opts">
306 <param name="UID_postprocessing" value="ensure"/>
307 <param name="TIC_DTA2D" value="false"/>
308 <param name="MGF_compact" value="false"/>
309 <param name="force_MaxQuant_compatibility" value="false"/>
310 <param name="force_TPP_compatibility" value="false"/>
311 <param name="convert_to_chromatograms" value="false"/>
312 <param name="change_im_format" value="none"/>
313 <param name="write_scan_index" value="true"/>
314 <param name="lossy_compression" value="false"/>
315 <param name="lossy_mass_accuracy" value="-1.0"/>
316 <param name="process_lowmemory" value="false"/>
317 <param name="no_peak_picking" value="false"/>
318 <param name="force" value="false"/>
319 <param name="test" value="true"/>
320 </section>
321 <param name="in" value="FileConverter_8_input.mzML"/>
322 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
323 <param name="out_type" value="mzData"/>
324 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
325 <output name="ctd_out" ftype="xml">
326 <assert_contents>
327 <is_valid_xml/>
328 </assert_contents>
329 </output>
330 </test>
331 <!-- TOPP_FileConverter_9 -->
332 <test expect_num_outputs="2">
333 <section name="adv_opts">
334 <param name="UID_postprocessing" value="ensure"/>
335 <param name="TIC_DTA2D" value="false"/>
336 <param name="MGF_compact" value="false"/>
337 <param name="force_MaxQuant_compatibility" value="false"/>
338 <param name="force_TPP_compatibility" value="false"/>
339 <param name="convert_to_chromatograms" value="false"/>
340 <param name="change_im_format" value="none"/>
341 <param name="write_scan_index" value="true"/>
342 <param name="lossy_compression" value="false"/>
343 <param name="lossy_mass_accuracy" value="-1.0"/>
344 <param name="process_lowmemory" value="false"/>
345 <param name="no_peak_picking" value="false"/>
346 <param name="force" value="false"/>
347 <param name="test" value="true"/>
348 </section>
349 <param name="in" value="FileConverter_9_input.consensusXML"/>
350 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
351 <param name="out_type" value="featureXML"/>
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 </test>
359 <!-- TOPP_FileConverter_10 -->
360 <test expect_num_outputs="2">
361 <section name="adv_opts">
362 <param name="UID_postprocessing" value="ensure"/>
363 <param name="TIC_DTA2D" value="false"/>
364 <param name="MGF_compact" value="false"/>
365 <param name="force_MaxQuant_compatibility" value="false"/>
366 <param name="force_TPP_compatibility" value="false"/>
367 <param name="convert_to_chromatograms" value="false"/>
368 <param name="change_im_format" value="none"/>
369 <param name="write_scan_index" value="true"/>
370 <param name="lossy_compression" value="false"/>
371 <param name="lossy_mass_accuracy" value="-1.0"/>
372 <param name="process_lowmemory" value="false"/>
373 <param name="no_peak_picking" value="false"/>
374 <param name="force" value="false"/>
375 <param name="test" value="true"/>
376 </section>
377 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
378 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
379 <param name="out_type" value="featureXML"/>
380 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
381 <output name="ctd_out" ftype="xml">
382 <assert_contents>
383 <is_valid_xml/>
384 </assert_contents>
385 </output>
386 </test>
387 <!-- TOPP_FileConverter_11 -->
388 <test expect_num_outputs="2">
389 <section name="adv_opts">
390 <param name="UID_postprocessing" value="ensure"/>
391 <param name="TIC_DTA2D" value="false"/>
392 <param name="MGF_compact" value="false"/>
393 <param name="force_MaxQuant_compatibility" value="false"/>
394 <param name="force_TPP_compatibility" value="false"/>
395 <param name="convert_to_chromatograms" value="false"/>
396 <param name="change_im_format" value="none"/>
397 <param name="write_scan_index" value="true"/>
398 <param name="lossy_compression" value="false"/>
399 <param name="lossy_mass_accuracy" value="-1.0"/>
400 <param name="process_lowmemory" value="false"/>
401 <param name="no_peak_picking" value="false"/>
402 <param name="force" value="false"/>
403 <param name="test" value="true"/>
404 </section>
405 <param name="in" value="FileConverter_11_input.peplist"/>
406 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
407 <param name="out_type" value="featureXML"/>
408 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
409 <output name="ctd_out" ftype="xml">
410 <assert_contents>
411 <is_valid_xml/>
412 </assert_contents>
413 </output>
414 </test>
415 <!-- TOPP_FileConverter_12 -->
416 <test expect_num_outputs="2">
417 <section name="adv_opts">
418 <param name="UID_postprocessing" value="ensure"/>
419 <param name="TIC_DTA2D" value="false"/>
420 <param name="MGF_compact" value="false"/>
421 <param name="force_MaxQuant_compatibility" value="false"/>
422 <param name="force_TPP_compatibility" value="false"/>
423 <param name="convert_to_chromatograms" value="false"/>
424 <param name="change_im_format" value="none"/>
425 <param name="write_scan_index" value="true"/>
426 <param name="lossy_compression" value="false"/>
427 <param name="lossy_mass_accuracy" value="-1.0"/>
428 <param name="process_lowmemory" value="false"/>
429 <param name="no_peak_picking" value="false"/>
430 <param name="force" value="false"/>
431 <param name="test" value="true"/>
432 </section>
433 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
434 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
435 <param name="out_type" value="featureXML"/>
436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
437 <output name="ctd_out" ftype="xml">
438 <assert_contents>
439 <is_valid_xml/>
440 </assert_contents>
441 </output>
442 </test>
443 <!-- TOPP_FileConverter_13 -->
444 <test expect_num_outputs="2">
445 <section name="adv_opts">
446 <param name="UID_postprocessing" value="ensure"/>
447 <param name="TIC_DTA2D" value="false"/>
448 <param name="MGF_compact" value="false"/>
449 <param name="force_MaxQuant_compatibility" value="false"/>
450 <param name="force_TPP_compatibility" value="false"/>
451 <param name="convert_to_chromatograms" value="false"/>
452 <param name="change_im_format" value="none"/>
453 <param name="write_scan_index" value="true"/>
454 <param name="lossy_compression" value="false"/>
455 <param name="lossy_mass_accuracy" value="-1.0"/>
456 <param name="process_lowmemory" value="false"/>
457 <param name="no_peak_picking" value="false"/>
458 <param name="force" value="false"/>
459 <param name="test" value="true"/>
460 </section>
461 <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
462 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
463 <param name="out_type" value="featureXML"/>
464 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
465 <output name="ctd_out" ftype="xml">
466 <assert_contents>
467 <is_valid_xml/>
468 </assert_contents>
469 </output>
470 </test>
471 <!-- TOPP_FileConverter_14 -->
472 <test expect_num_outputs="2">
473 <section name="adv_opts">
474 <param name="UID_postprocessing" value="ensure"/>
475 <param name="TIC_DTA2D" value="false"/>
476 <param name="MGF_compact" value="false"/>
477 <param name="force_MaxQuant_compatibility" value="false"/>
478 <param name="force_TPP_compatibility" value="false"/>
479 <param name="convert_to_chromatograms" value="false"/>
480 <param name="change_im_format" value="none"/>
481 <param name="write_scan_index" value="true"/>
482 <param name="lossy_compression" value="false"/>
483 <param name="lossy_mass_accuracy" value="-1.0"/>
484 <param name="process_lowmemory" value="false"/>
485 <param name="no_peak_picking" value="false"/>
486 <param name="force" value="false"/>
487 <param name="test" value="true"/>
488 </section>
489 <param name="in" value="FileConverter_9_output.featureXML"/>
490 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
491 <param name="out_type" value="consensusXML"/>
492 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
493 <output name="ctd_out" ftype="xml">
494 <assert_contents>
495 <is_valid_xml/>
496 </assert_contents>
497 </output>
498 </test>
499 <!-- TOPP_FileConverter_15 -->
500 <test expect_num_outputs="2">
501 <section name="adv_opts">
502 <param name="UID_postprocessing" value="ensure"/>
503 <param name="TIC_DTA2D" value="false"/>
504 <param name="MGF_compact" value="false"/>
505 <param name="force_MaxQuant_compatibility" value="false"/>
506 <param name="force_TPP_compatibility" value="false"/>
507 <param name="convert_to_chromatograms" value="false"/>
508 <param name="change_im_format" value="none"/>
509 <param name="write_scan_index" value="true"/>
510 <param name="lossy_compression" value="false"/>
511 <param name="lossy_mass_accuracy" value="-1.0"/>
512 <param name="process_lowmemory" value="false"/>
513 <param name="no_peak_picking" value="false"/>
514 <param name="force" value="false"/>
515 <param name="test" value="true"/>
516 </section>
517 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
518 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
519 <param name="out_type" value="consensusXML"/>
520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
521 <output name="ctd_out" ftype="xml">
522 <assert_contents>
523 <is_valid_xml/>
524 </assert_contents>
525 </output>
526 </test>
527 <!-- TOPP_FileConverter_16 -->
528 <test expect_num_outputs="2">
529 <section name="adv_opts">
530 <param name="UID_postprocessing" value="ensure"/>
531 <param name="TIC_DTA2D" value="false"/>
532 <param name="MGF_compact" value="false"/>
533 <param name="force_MaxQuant_compatibility" value="false"/>
534 <param name="force_TPP_compatibility" value="false"/>
535 <param name="convert_to_chromatograms" value="false"/>
536 <param name="change_im_format" value="none"/>
537 <param name="write_scan_index" value="true"/>
538 <param name="lossy_compression" value="false"/>
539 <param name="lossy_mass_accuracy" value="-1.0"/>
540 <param name="process_lowmemory" value="false"/>
541 <param name="no_peak_picking" value="false"/>
542 <param name="force" value="false"/>
543 <param name="test" value="true"/>
544 </section>
545 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
546 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
547 <param name="out_type" value="consensusXML"/>
548 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
549 <output name="ctd_out" ftype="xml">
550 <assert_contents>
551 <is_valid_xml/>
552 </assert_contents>
553 </output>
554 </test>
555 <!-- TOPP_FileConverter_17 -->
556 <test expect_num_outputs="2">
557 <section name="adv_opts">
558 <param name="UID_postprocessing" value="ensure"/>
559 <param name="TIC_DTA2D" value="false"/>
560 <param name="MGF_compact" value="false"/>
561 <param name="force_MaxQuant_compatibility" value="false"/>
562 <param name="force_TPP_compatibility" value="false"/>
563 <param name="convert_to_chromatograms" value="false"/>
564 <param name="change_im_format" value="none"/>
565 <param name="write_scan_index" value="true"/>
566 <param name="lossy_compression" value="false"/>
567 <param name="lossy_mass_accuracy" value="-1.0"/>
568 <param name="process_lowmemory" value="false"/>
569 <param name="no_peak_picking" value="false"/>
570 <param name="force" value="false"/>
571 <param name="test" value="true"/>
572 </section>
573 <param name="in" value="FileConverter_17_input.consensusXML"/>
574 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
575 <param name="out_type" value="csv"/>
576 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
577 <output name="ctd_out" ftype="xml">
578 <assert_contents>
579 <is_valid_xml/>
580 </assert_contents>
581 </output>
582 </test>
583 <!-- TOPP_FileConverter_18 -->
584 <test expect_num_outputs="2">
585 <section name="adv_opts">
586 <param name="UID_postprocessing" value="ensure"/>
587 <param name="TIC_DTA2D" value="false"/>
588 <param name="MGF_compact" value="false"/>
589 <param name="force_MaxQuant_compatibility" value="false"/>
590 <param name="force_TPP_compatibility" value="false"/>
591 <param name="convert_to_chromatograms" value="false"/>
592 <param name="change_im_format" value="none"/>
593 <param name="write_scan_index" value="true"/>
594 <param name="lossy_compression" value="false"/>
595 <param name="lossy_mass_accuracy" value="-1.0"/>
596 <param name="process_lowmemory" value="false"/>
597 <param name="no_peak_picking" value="false"/>
598 <param name="force" value="false"/>
599 <param name="test" value="true"/>
600 </section>
601 <param name="in" value="FileConverter_17_input.consensusXML"/>
602 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
603 <param name="out_type" value="csv"/>
604 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
605 <output name="ctd_out" ftype="xml">
606 <assert_contents>
607 <is_valid_xml/>
608 </assert_contents>
609 </output>
610 </test>
611 <!-- TOPP_FileConverter_19 -->
612 <test expect_num_outputs="2">
613 <section name="adv_opts">
614 <param name="UID_postprocessing" value="ensure"/>
615 <param name="TIC_DTA2D" value="false"/>
616 <param name="MGF_compact" value="false"/>
617 <param name="force_MaxQuant_compatibility" value="false"/>
618 <param name="force_TPP_compatibility" value="false"/>
619 <param name="convert_to_chromatograms" value="false"/>
620 <param name="change_im_format" value="none"/>
621 <param name="write_scan_index" value="true"/>
622 <param name="lossy_compression" value="false"/>
623 <param name="lossy_mass_accuracy" value="-1.0"/>
624 <param name="process_lowmemory" value="true"/>
625 <param name="no_peak_picking" value="false"/>
626 <param name="force" value="false"/>
627 <param name="test" value="true"/>
628 </section>
629 <param name="in" value="FileFilter_1_input.mzML"/>
630 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
631 <param name="out_type" value="mzML"/>
632 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
633 <output name="ctd_out" ftype="xml">
634 <assert_contents>
635 <is_valid_xml/>
636 </assert_contents>
637 </output>
638 </test>
639 <!-- TOPP_FileConverter_20 -->
640 <test expect_num_outputs="2">
641 <section name="adv_opts">
642 <param name="UID_postprocessing" value="ensure"/>
643 <param name="TIC_DTA2D" value="false"/>
644 <param name="MGF_compact" value="false"/>
645 <param name="force_MaxQuant_compatibility" value="false"/>
646 <param name="force_TPP_compatibility" value="false"/>
647 <param name="convert_to_chromatograms" value="false"/>
648 <param name="change_im_format" value="none"/>
649 <param name="write_scan_index" value="true"/>
650 <param name="lossy_compression" value="false"/>
651 <param name="lossy_mass_accuracy" value="-1.0"/>
652 <param name="process_lowmemory" value="false"/>
653 <param name="no_peak_picking" value="false"/>
654 <param name="force" value="false"/>
655 <param name="test" value="true"/>
656 </section>
657 <param name="in" value="FileConverter_20_input.featureXML"/>
658 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
659 <param name="out_type" value="featureXML"/>
660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
661 <output name="ctd_out" ftype="xml">
662 <assert_contents>
663 <is_valid_xml/>
664 </assert_contents>
665 </output>
666 </test>
667 <!-- TOPP_FileConverter_21 -->
668 <test expect_num_outputs="2">
669 <section name="adv_opts">
670 <param name="UID_postprocessing" value="ensure"/>
671 <param name="TIC_DTA2D" value="false"/>
672 <param name="MGF_compact" value="false"/>
673 <param name="force_MaxQuant_compatibility" value="false"/>
674 <param name="force_TPP_compatibility" value="false"/>
675 <param name="convert_to_chromatograms" value="false"/>
676 <param name="change_im_format" value="none"/>
677 <param name="write_scan_index" value="true"/>
678 <param name="lossy_compression" value="false"/>
679 <param name="lossy_mass_accuracy" value="-1.0"/>
680 <param name="process_lowmemory" value="true"/>
681 <param name="no_peak_picking" value="false"/>
682 <param name="force" value="false"/>
683 <param name="test" value="true"/>
684 </section>
685 <param name="in" value="FileConverter_4_input.mzXML"/>
686 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
687 <param name="out_type" value="mzML"/>
688 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
689 <output name="ctd_out" ftype="xml">
690 <assert_contents>
691 <is_valid_xml/>
692 </assert_contents>
693 </output>
694 </test>
695 <!-- TOPP_FileConverter_23 -->
696 <test expect_num_outputs="2">
697 <section name="adv_opts">
698 <param name="UID_postprocessing" value="ensure"/>
699 <param name="TIC_DTA2D" value="false"/>
700 <param name="MGF_compact" value="false"/>
701 <param name="force_MaxQuant_compatibility" value="false"/>
702 <param name="force_TPP_compatibility" value="false"/>
703 <param name="convert_to_chromatograms" value="false"/>
704 <param name="change_im_format" value="none"/>
705 <param name="write_scan_index" value="true"/>
706 <param name="lossy_compression" value="false"/>
707 <param name="lossy_mass_accuracy" value="-1.0"/>
708 <param name="process_lowmemory" value="false"/>
709 <param name="no_peak_picking" value="false"/>
710 <param name="force" value="false"/>
711 <param name="test" value="true"/>
712 </section>
713 <param name="in" value="FileConverter_23_input.mzML"/>
714 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
715 <param name="out_type" value="mzML"/>
716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
717 <output name="ctd_out" ftype="xml">
718 <assert_contents>
719 <is_valid_xml/>
720 </assert_contents>
721 </output>
722 </test>
723 <!-- TOPP_FileConverter_24 -->
724 <test expect_num_outputs="2">
725 <section name="adv_opts">
726 <param name="UID_postprocessing" value="ensure"/>
727 <param name="TIC_DTA2D" value="false"/>
728 <param name="MGF_compact" value="false"/>
729 <param name="force_MaxQuant_compatibility" value="false"/>
730 <param name="force_TPP_compatibility" value="false"/>
731 <param name="convert_to_chromatograms" value="false"/>
732 <param name="change_im_format" value="none"/>
733 <param name="write_scan_index" value="true"/>
734 <param name="lossy_compression" value="true"/>
735 <param name="lossy_mass_accuracy" value="0.0001"/>
736 <param name="process_lowmemory" value="true"/>
737 <param name="no_peak_picking" value="false"/>
738 <param name="force" value="false"/>
739 <param name="test" value="true"/>
740 </section>
741 <param name="in" value="FileFilter_1_input.mzML"/>
742 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
743 <param name="out_type" value="mzML"/>
744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
745 <output name="ctd_out" ftype="xml">
746 <assert_contents>
747 <is_valid_xml/>
748 </assert_contents>
749 </output>
750 </test>
751 <!-- TOPP_FileConverter_25 -->
752 <test expect_num_outputs="2">
753 <section name="adv_opts">
754 <param name="UID_postprocessing" value="ensure"/>
755 <param name="TIC_DTA2D" value="false"/>
756 <param name="MGF_compact" value="false"/>
757 <param name="force_MaxQuant_compatibility" value="false"/>
758 <param name="force_TPP_compatibility" value="false"/>
759 <param name="convert_to_chromatograms" value="false"/>
760 <param name="change_im_format" value="none"/>
761 <param name="write_scan_index" value="true"/>
762 <param name="lossy_compression" value="true"/>
763 <param name="lossy_mass_accuracy" value="-1.0"/>
764 <param name="process_lowmemory" value="true"/>
765 <param name="no_peak_picking" value="false"/>
766 <param name="force" value="false"/>
767 <param name="test" value="true"/>
768 </section>
769 <param name="in" value="FileFilter_1_input.mzML"/>
770 <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
771 <param name="out_type" value="mzML"/>
772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
773 <output name="ctd_out" ftype="xml">
774 <assert_contents>
775 <is_valid_xml/>
776 </assert_contents>
777 </output>
778 </test>
779 <!-- TOPP_FileConverter_26 -->
780 <test expect_num_outputs="2">
781 <section name="adv_opts">
782 <param name="UID_postprocessing" value="ensure"/>
783 <param name="TIC_DTA2D" value="false"/>
784 <param name="MGF_compact" value="false"/>
785 <param name="force_MaxQuant_compatibility" value="true"/>
786 <param name="force_TPP_compatibility" value="false"/>
787 <param name="convert_to_chromatograms" value="false"/>
788 <param name="change_im_format" value="none"/>
789 <param name="write_scan_index" value="true"/>
790 <param name="lossy_compression" value="false"/>
791 <param name="lossy_mass_accuracy" value="-1.0"/>
792 <param name="process_lowmemory" value="false"/>
793 <param name="no_peak_picking" value="false"/>
794 <param name="force" value="false"/>
795 <param name="test" value="true"/>
796 </section>
797 <param name="in" value="FileFilter_1_input.mzML"/>
798 <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
799 <param name="out_type" value="mzXML"/>
800 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
801 <output name="ctd_out" ftype="xml">
802 <assert_contents>
803 <is_valid_xml/>
804 </assert_contents>
805 </output>
806 </test>
807 <!-- TOPP_FileConverter_26-2 -->
808 <test expect_num_outputs="2">
809 <section name="adv_opts">
810 <param name="UID_postprocessing" value="ensure"/>
811 <param name="TIC_DTA2D" value="false"/>
812 <param name="MGF_compact" value="false"/>
813 <param name="force_MaxQuant_compatibility" value="true"/>
814 <param name="force_TPP_compatibility" value="false"/>
815 <param name="convert_to_chromatograms" value="false"/>
816 <param name="change_im_format" value="none"/>
817 <param name="write_scan_index" value="true"/>
818 <param name="lossy_compression" value="false"/>
819 <param name="lossy_mass_accuracy" value="-1.0"/>
820 <param name="process_lowmemory" value="false"/>
821 <param name="no_peak_picking" value="false"/>
822 <param name="force" value="false"/>
823 <param name="test" value="true"/>
824 </section>
825 <param name="in" value="FileConverter_26_output.mzXML"/>
826 <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
827 <param name="out_type" value="mzXML"/>
828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
829 <output name="ctd_out" ftype="xml">
830 <assert_contents>
831 <is_valid_xml/>
832 </assert_contents>
833 </output>
834 </test>
835 <!-- TOPP_FileConverter_27 -->
836 <test expect_num_outputs="2">
837 <section name="adv_opts">
838 <param name="UID_postprocessing" value="ensure"/>
839 <param name="TIC_DTA2D" value="false"/>
840 <param name="MGF_compact" value="false"/>
841 <param name="force_MaxQuant_compatibility" value="false"/>
842 <param name="force_TPP_compatibility" value="false"/>
843 <param name="convert_to_chromatograms" value="true"/>
844 <param name="change_im_format" value="none"/>
845 <param name="write_scan_index" value="true"/>
846 <param name="lossy_compression" value="false"/>
847 <param name="lossy_mass_accuracy" value="-1.0"/>
848 <param name="process_lowmemory" value="false"/>
849 <param name="no_peak_picking" value="false"/>
850 <param name="force" value="false"/>
851 <param name="test" value="true"/>
852 </section>
853 <param name="in" value="FileConverter_27_input.mzML"/>
854 <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
855 <param name="out_type" value="mzML"/>
856 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
857 <output name="ctd_out" ftype="xml">
858 <assert_contents>
859 <is_valid_xml/>
860 </assert_contents>
861 </output>
862 </test>
863 <!-- TOPP_FileConverter_28 -->
864 <test expect_num_outputs="2">
865 <section name="adv_opts">
866 <param name="UID_postprocessing" value="ensure"/>
867 <param name="TIC_DTA2D" value="false"/>
868 <param name="MGF_compact" value="false"/>
869 <param name="force_MaxQuant_compatibility" value="false"/>
870 <param name="force_TPP_compatibility" value="false"/>
871 <param name="convert_to_chromatograms" value="true"/>
872 <param name="change_im_format" value="none"/>
873 <param name="write_scan_index" value="true"/>
874 <param name="lossy_compression" value="false"/>
875 <param name="lossy_mass_accuracy" value="-1.0"/>
876 <param name="process_lowmemory" value="false"/>
877 <param name="no_peak_picking" value="false"/>
878 <param name="force" value="false"/>
879 <param name="test" value="true"/>
880 </section>
881 <param name="in" value="FileConverter_28_input.mzML"/>
882 <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
883 <param name="out_type" value="mzML"/>
884 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
885 <output name="ctd_out" ftype="xml">
886 <assert_contents>
887 <is_valid_xml/>
888 </assert_contents>
889 </output>
890 </test>
891 <!-- TOPP_FileConverter_29 -->
892 <test expect_num_outputs="2">
893 <section name="adv_opts">
894 <param name="UID_postprocessing" value="ensure"/>
895 <param name="TIC_DTA2D" value="false"/>
896 <param name="MGF_compact" value="false"/>
897 <param name="force_MaxQuant_compatibility" value="false"/>
898 <param name="force_TPP_compatibility" value="false"/>
899 <param name="convert_to_chromatograms" value="false"/>
900 <param name="change_im_format" value="none"/>
901 <param name="write_scan_index" value="true"/>
902 <param name="lossy_compression" value="true"/>
903 <param name="lossy_mass_accuracy" value="1e-05"/>
904 <param name="process_lowmemory" value="true"/>
905 <param name="no_peak_picking" value="false"/>
906 <param name="force" value="false"/>
907 <param name="test" value="true"/>
908 </section>
909 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
910 <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
911 <param name="out_type" value="mzML"/>
912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
913 <output name="ctd_out" ftype="xml">
914 <assert_contents>
915 <is_valid_xml/>
916 </assert_contents>
917 </output>
918 </test>
919 <!-- TOPP_FileConverter_29_back -->
920 <test expect_num_outputs="2">
921 <section name="adv_opts">
922 <param name="UID_postprocessing" value="ensure"/>
923 <param name="TIC_DTA2D" value="false"/>
924 <param name="MGF_compact" value="false"/>
925 <param name="force_MaxQuant_compatibility" value="false"/>
926 <param name="force_TPP_compatibility" value="false"/>
927 <param name="convert_to_chromatograms" value="false"/>
928 <param name="change_im_format" value="none"/>
929 <param name="write_scan_index" value="true"/>
930 <param name="lossy_compression" value="false"/>
931 <param name="lossy_mass_accuracy" value="-1.0"/>
932 <param name="process_lowmemory" value="false"/>
933 <param name="no_peak_picking" value="false"/>
934 <param name="force" value="false"/>
935 <param name="test" value="true"/>
936 </section>
937 <param name="in" value="FileConverter_29_output.mzML"/>
938 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
939 <param name="out_type" value="mzML"/>
940 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
941 <output name="ctd_out" ftype="xml">
942 <assert_contents>
943 <is_valid_xml/>
944 </assert_contents>
945 </output>
946 </test>
947 <!-- TOPP_FileConverter_30 -->
948 <test expect_num_outputs="2">
949 <section name="adv_opts">
950 <param name="UID_postprocessing" value="ensure"/>
951 <param name="TIC_DTA2D" value="false"/>
952 <param name="MGF_compact" value="false"/>
953 <param name="force_MaxQuant_compatibility" value="false"/>
954 <param name="force_TPP_compatibility" value="false"/>
955 <param name="convert_to_chromatograms" value="false"/>
956 <param name="change_im_format" value="multiple_spectra"/>
957 <param name="write_scan_index" value="true"/>
958 <param name="lossy_compression" value="false"/>
959 <param name="lossy_mass_accuracy" value="-1.0"/>
960 <param name="process_lowmemory" value="false"/>
961 <param name="no_peak_picking" value="false"/>
962 <param name="force" value="false"/>
963 <param name="test" value="true"/>
964 </section>
965 <param name="in" value="FileConverter_30_input.mzML"/>
966 <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
967 <param name="out_type" value="mzML"/>
968 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
969 <output name="ctd_out" ftype="xml">
970 <assert_contents>
971 <is_valid_xml/>
972 </assert_contents>
973 </output>
974 </test>
975 <!-- TOPP_FileConverter_31 -->
976 <test expect_num_outputs="2">
977 <section name="adv_opts">
978 <param name="UID_postprocessing" value="ensure"/>
979 <param name="TIC_DTA2D" value="false"/>
980 <param name="MGF_compact" value="false"/>
981 <param name="force_MaxQuant_compatibility" value="false"/>
982 <param name="force_TPP_compatibility" value="false"/>
983 <param name="convert_to_chromatograms" value="false"/>
984 <param name="change_im_format" value="concatenated"/>
985 <param name="write_scan_index" value="true"/>
986 <param name="lossy_compression" value="false"/>
987 <param name="lossy_mass_accuracy" value="-1.0"/>
988 <param name="process_lowmemory" value="false"/>
989 <param name="no_peak_picking" value="false"/>
990 <param name="force" value="false"/>
991 <param name="test" value="true"/>
992 </section>
993 <param name="in" value="FileConverter_30_output.mzML"/>
994 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
995 <param name="out_type" value="mzML"/>
996 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
997 <output name="ctd_out" ftype="xml">
998 <assert_contents>
999 <is_valid_xml/>
1000 </assert_contents>
1001 </output>
1002 </test>
1003 <!-- TOPP_FileConverter_32 -->
1004 <test expect_num_outputs="2">
1005 <section name="adv_opts">
1006 <param name="UID_postprocessing" value="ensure"/>
1007 <param name="TIC_DTA2D" value="false"/>
1008 <param name="MGF_compact" value="false"/>
1009 <param name="force_MaxQuant_compatibility" value="false"/>
1010 <param name="force_TPP_compatibility" value="false"/>
1011 <param name="convert_to_chromatograms" value="false"/>
1012 <param name="change_im_format" value="none"/>
1013 <param name="write_scan_index" value="true"/>
1014 <param name="lossy_compression" value="false"/>
1015 <param name="lossy_mass_accuracy" value="-1.0"/>
1016 <param name="process_lowmemory" value="false"/>
1017 <param name="no_peak_picking" value="false"/>
1018 <param name="force" value="false"/>
1019 <param name="test" value="true"/>
1020 </section>
1021 <param name="in" value="FileConverter_32_input.mzML"/>
1022 <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1023 <param name="out_type" value="mzML"/>
1024 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1025 <output name="ctd_out" ftype="xml">
1026 <assert_contents>
1027 <is_valid_xml/>
1028 </assert_contents>
1029 </output>
1030 </test>
1031 <!-- TOPP_IDFileConverter_32_File_Conversion -->
1032 <test expect_num_outputs="2">
1033 <section name="adv_opts">
1034 <param name="UID_postprocessing" value="ensure"/>
1035 <param name="TIC_DTA2D" value="false"/>
1036 <param name="MGF_compact" value="false"/>
1037 <param name="force_MaxQuant_compatibility" value="false"/>
1038 <param name="force_TPP_compatibility" value="false"/>
1039 <param name="convert_to_chromatograms" value="false"/>
1040 <param name="change_im_format" value="none"/>
1041 <param name="write_scan_index" value="true"/>
1042 <param name="lossy_compression" value="false"/>
1043 <param name="lossy_mass_accuracy" value="-1.0"/>
1044 <param name="process_lowmemory" value="false"/>
1045 <param name="no_peak_picking" value="false"/>
1046 <param name="force" value="false"/>
1047 <param name="test" value="true"/>
1048 </section>
1049 <param name="in" value="IDFileConverter_32_output.tmp"/>
1050 <output name="out" file="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
1051 <param name="out_type" value="mgf"/>
1052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1053 <output name="ctd_out" ftype="xml">
1054 <assert_contents>
1055 <is_valid_xml/>
1056 </assert_contents>
1057 </output>
1058 </test>
1059 <!-- TOPP_IDFileConverter_33_File_Conversion -->
1060 <test expect_num_outputs="2">
1061 <section name="adv_opts">
1062 <param name="UID_postprocessing" value="ensure"/>
1063 <param name="TIC_DTA2D" value="false"/>
1064 <param name="MGF_compact" value="false"/>
1065 <param name="force_MaxQuant_compatibility" value="false"/>
1066 <param name="force_TPP_compatibility" value="false"/>
1067 <param name="convert_to_chromatograms" value="false"/>
1068 <param name="change_im_format" value="none"/>
1069 <param name="write_scan_index" value="true"/>
1070 <param name="lossy_compression" value="false"/>
1071 <param name="lossy_mass_accuracy" value="-1.0"/>
1072 <param name="process_lowmemory" value="false"/>
1073 <param name="no_peak_picking" value="false"/>
1074 <param name="force" value="false"/>
1075 <param name="test" value="true"/>
1076 </section>
1077 <param name="in" value="IDFileConverter_33_output.tmp"/>
1078 <output name="out" file="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
1079 <param name="out_type" value="mgf"/>
1080 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1081 <output name="ctd_out" ftype="xml">
1082 <assert_contents>
1083 <is_valid_xml/>
1084 </assert_contents>
1085 </output>
1086 </test>
1087 <!-- TOPP_THERMORAWFILEPARSER_1 -->
1088 <test expect_num_outputs="2">
1089 <section name="adv_opts">
1090 <param name="UID_postprocessing" value="ensure"/>
1091 <param name="TIC_DTA2D" value="false"/>
1092 <param name="MGF_compact" value="false"/>
1093 <param name="force_MaxQuant_compatibility" value="false"/>
1094 <param name="force_TPP_compatibility" value="false"/>
1095 <param name="convert_to_chromatograms" value="false"/>
1096 <param name="change_im_format" value="none"/>
1097 <param name="write_scan_index" value="true"/>
1098 <param name="lossy_compression" value="false"/>
1099 <param name="lossy_mass_accuracy" value="-1.0"/>
1100 <param name="process_lowmemory" value="false"/>
1101 <param name="no_peak_picking" value="false"/>
1102 <param name="force" value="false"/>
1103 <param name="test" value="true"/>
1104 </section>
1105 <param name="in" value="ginkgotoxin-ms-switching.raw"/>
1106 <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1107 <param name="out_type" value="mzML"/>
1108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1109 <output name="ctd_out" ftype="xml">
1110 <assert_contents>
1111 <is_valid_xml/>
1112 </assert_contents>
1113 </output>
1114 </test>
1115 <test expect_num_outputs="1">
1116 <param name="in" value="FileConverter_1_input.mzData"/>
1117 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1118 <param name="out_type" value="mzML"/>
1119 </test>
1120 </tests>
111 <help><![CDATA[Converts between different MS file formats. 1121 <help><![CDATA[Converts between different MS file formats.
112 1122
113 1123
114 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileConverter.html]]></help> 1124 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileConverter.html]]></help>
115 <expand macro="references"/> 1125 <expand macro="references"/>
116 </tool> 1126 </tool>