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comparison FileConverter.xml @ 16:8b6336c903ef draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:33:58 +0000
parents 2a93a25f0599
children
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15:2a93a25f0599 16:8b6336c903ef
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converts between different MS file formats.</description> 4 <description>Converts between different MS file formats</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FileConverter</token> 6 <token name="@EXECUTABLE@">FileConverter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="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)"/> 41 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" 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)"/>
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"> 42 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
44 <option value="consensusXML">consensusxml</option> 43 <option value="consensusXML">consensusxml</option>
45 <option value="csv">csv</option> 44 <option value="csv">csv</option>
46 <option value="dta2d">dta2d</option> 45 <option value="dta2d">dta2d</option>
47 <option value="edta">edta</option> 46 <option value="edta">edta</option>
48 <option value="featureXML">featurexml</option> 47 <option value="featureXML">featurexml</option>
49 <option value="mgf">mgf</option> 48 <option value="mgf">mgf</option>
50 <option value="mzData">mzdata</option> 49 <option value="mzData">mzdata</option>
51 <option value="mzML">mzml</option> 50 <option value="mzML">mzml</option>
52 <option value="mzXML">mzxml</option> 51 <option value="mzXML">mzxml</option>
53 <option value="oms">sqlite (oms)</option> 52 <option value="oms">sqlite (oms)</option>
53 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
54 <expand macro="list_string_san" name="out_type"/> 54 <expand macro="list_string_san" name="out_type"/>
55 </param> 55 </param>
56 <expand macro="adv_opts_macro"> 56 <expand macro="adv_opts_macro">
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"> 57 <param argument="-UID_postprocessing" type="select" 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">
58 <option value="none">none</option> 58 <option value="none">none</option>
59 <option value="ensure" selected="true">ensure</option> 59 <option value="ensure" selected="true">ensure</option>
60 <option value="reassign">reassign</option> 60 <option value="reassign">reassign</option>
61 <expand macro="list_string_san" name="UID_postprocessing"/> 61 <expand macro="list_string_san" name="UID_postprocessing"/>
62 </param> 62 </param>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""> 68 <param argument="-change_im_format" type="select" 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="">
69 <option value="none" selected="true">none</option> 69 <option value="none" selected="true">none</option>
70 <option value="concatenated">concatenated</option> 70 <option value="concatenated">concatenated</option>
71 <option value="multiple_spectra">multiple_spectra</option> 71 <option value="multiple_spectra">multiple_spectra</option>
72 <option value="mixed">mixed</option> 72 <option value="mixed">mixed</option>
73 <expand macro="list_string_san" name="change_im_format"/> 73 <expand macro="list_string_san" name="change_im_format"/>
74 </param> 74 </param>
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"/> 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 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 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" 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 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 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 argument="-no_zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables zlib compression for raw file conversion" help="Enables compatibility with some tools that do not support compressed input files, e.g. X!Tandem"/>
81 <param argument="-include_noise" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include noise data in mzML output" help=""/>
80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 82 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 83 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
82 <expand macro="list_string_san" name="test"/> 84 <expand macro="list_string_san" name="test"/>
83 </param> 85 </param>
84 </expand> 86 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 87 <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> 88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
102 </data> 104 </data>
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
105 </data> 107 </data>
106 </outputs> 108 </outputs>
107 <tests><!-- TOPP_FileConverter_1 --> 109 <tests>
108 <test expect_num_outputs="2"> 110 <!-- TOPP_FileConverter_1 -->
109 <section name="adv_opts"> 111 <test expect_num_outputs="2">
110 <param name="UID_postprocessing" value="ensure"/> 112 <section name="adv_opts">
111 <param name="TIC_DTA2D" value="false"/> 113 <param name="UID_postprocessing" value="ensure"/>
112 <param name="MGF_compact" value="false"/> 114 <param name="TIC_DTA2D" value="false"/>
113 <param name="force_MaxQuant_compatibility" value="false"/> 115 <param name="MGF_compact" value="false"/>
114 <param name="force_TPP_compatibility" value="false"/> 116 <param name="force_MaxQuant_compatibility" value="false"/>
115 <param name="convert_to_chromatograms" value="false"/> 117 <param name="force_TPP_compatibility" value="false"/>
116 <param name="change_im_format" value="none"/> 118 <param name="convert_to_chromatograms" value="false"/>
117 <param name="write_scan_index" value="true"/> 119 <param name="change_im_format" value="none"/>
118 <param name="lossy_compression" value="false"/> 120 <param name="write_scan_index" value="true"/>
119 <param name="lossy_mass_accuracy" value="-1.0"/> 121 <param name="lossy_compression" value="false"/>
120 <param name="process_lowmemory" value="false"/> 122 <param name="lossy_mass_accuracy" value="-1.0"/>
121 <param name="no_peak_picking" value="false"/> 123 <param name="process_lowmemory" value="false"/>
124 <param name="no_peak_picking" value="false"/>
125 <param name="no_zlib_compression" value="false"/>
126 <param name="include_noise" value="false"/>
122 <param name="force" value="false"/> 127 <param name="force" value="false"/>
123 <param name="test" value="true"/> 128 <param name="test" value="true"/>
124 </section> 129 </section>
125 <param name="in" value="FileConverter_1_input.mzData"/> 130 <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"/> 131 <output name="out" value="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
127 <param name="out_type" value="mzML"/> 132 <param name="out_type" value="mzML"/>
128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 133 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
129 <output name="ctd_out" ftype="xml"> 134 <output name="ctd_out" ftype="xml">
130 <assert_contents> 135 <assert_contents>
131 <is_valid_xml/> 136 <is_valid_xml/>
132 </assert_contents> 137 </assert_contents>
133 </output> 138 </output>
139 <assert_stdout>
140 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
141 </assert_stdout>
134 </test> 142 </test>
135 <!-- TOPP_FileConverter_2 --> 143 <!-- TOPP_FileConverter_2 -->
136 <test expect_num_outputs="2"> 144 <test expect_num_outputs="2">
137 <section name="adv_opts"> 145 <section name="adv_opts">
138 <param name="UID_postprocessing" value="ensure"/> 146 <param name="UID_postprocessing" value="ensure"/>
145 <param name="write_scan_index" value="true"/> 153 <param name="write_scan_index" value="true"/>
146 <param name="lossy_compression" value="false"/> 154 <param name="lossy_compression" value="false"/>
147 <param name="lossy_mass_accuracy" value="-1.0"/> 155 <param name="lossy_mass_accuracy" value="-1.0"/>
148 <param name="process_lowmemory" value="false"/> 156 <param name="process_lowmemory" value="false"/>
149 <param name="no_peak_picking" value="false"/> 157 <param name="no_peak_picking" value="false"/>
158 <param name="no_zlib_compression" value="false"/>
159 <param name="include_noise" value="false"/>
150 <param name="force" value="false"/> 160 <param name="force" value="false"/>
151 <param name="test" value="true"/> 161 <param name="test" value="true"/>
152 </section> 162 </section>
153 <param name="in" value="FileConverter_2_input.someInputDTA2D"/> 163 <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"/> 164 <output name="out" value="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
155 <param name="out_type" value="mzML"/> 165 <param name="out_type" value="mzML"/>
156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
157 <output name="ctd_out" ftype="xml"> 167 <output name="ctd_out" ftype="xml">
158 <assert_contents> 168 <assert_contents>
159 <is_valid_xml/> 169 <is_valid_xml/>
160 </assert_contents> 170 </assert_contents>
161 </output> 171 </output>
172 <assert_stdout>
173 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
174 </assert_stdout>
162 </test> 175 </test>
163 <!-- TOPP_FileConverter_3 --> 176 <!-- TOPP_FileConverter_3 -->
164 <test expect_num_outputs="2"> 177 <test expect_num_outputs="2">
165 <section name="adv_opts"> 178 <section name="adv_opts">
166 <param name="UID_postprocessing" value="ensure"/> 179 <param name="UID_postprocessing" value="ensure"/>
173 <param name="write_scan_index" value="true"/> 186 <param name="write_scan_index" value="true"/>
174 <param name="lossy_compression" value="false"/> 187 <param name="lossy_compression" value="false"/>
175 <param name="lossy_mass_accuracy" value="-1.0"/> 188 <param name="lossy_mass_accuracy" value="-1.0"/>
176 <param name="process_lowmemory" value="false"/> 189 <param name="process_lowmemory" value="false"/>
177 <param name="no_peak_picking" value="false"/> 190 <param name="no_peak_picking" value="false"/>
191 <param name="no_zlib_compression" value="false"/>
192 <param name="include_noise" value="false"/>
178 <param name="force" value="false"/> 193 <param name="force" value="false"/>
179 <param name="test" value="true"/> 194 <param name="test" value="true"/>
180 </section> 195 </section>
181 <param name="in" value="FileConverter_3_input.featureXML"/> 196 <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"/> 197 <output name="out" value="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
183 <param name="out_type" value="mzML"/> 198 <param name="out_type" value="mzML"/>
184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
185 <output name="ctd_out" ftype="xml"> 200 <output name="ctd_out" ftype="xml">
186 <assert_contents> 201 <assert_contents>
187 <is_valid_xml/> 202 <is_valid_xml/>
188 </assert_contents> 203 </assert_contents>
189 </output> 204 </output>
205 <assert_stdout>
206 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
207 </assert_stdout>
190 </test> 208 </test>
191 <!-- TOPP_FileConverter_4 --> 209 <!-- TOPP_FileConverter_4 -->
192 <test expect_num_outputs="2"> 210 <test expect_num_outputs="2">
193 <section name="adv_opts"> 211 <section name="adv_opts">
194 <param name="UID_postprocessing" value="ensure"/> 212 <param name="UID_postprocessing" value="ensure"/>
201 <param name="write_scan_index" value="true"/> 219 <param name="write_scan_index" value="true"/>
202 <param name="lossy_compression" value="false"/> 220 <param name="lossy_compression" value="false"/>
203 <param name="lossy_mass_accuracy" value="-1.0"/> 221 <param name="lossy_mass_accuracy" value="-1.0"/>
204 <param name="process_lowmemory" value="false"/> 222 <param name="process_lowmemory" value="false"/>
205 <param name="no_peak_picking" value="false"/> 223 <param name="no_peak_picking" value="false"/>
224 <param name="no_zlib_compression" value="false"/>
225 <param name="include_noise" value="false"/>
206 <param name="force" value="false"/> 226 <param name="force" value="false"/>
207 <param name="test" value="true"/> 227 <param name="test" value="true"/>
208 </section> 228 </section>
209 <param name="in" value="FileConverter_4_input.mzXML"/> 229 <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"/> 230 <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
211 <param name="out_type" value="mzML"/> 231 <param name="out_type" value="mzML"/>
212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
213 <output name="ctd_out" ftype="xml"> 233 <output name="ctd_out" ftype="xml">
214 <assert_contents> 234 <assert_contents>
215 <is_valid_xml/> 235 <is_valid_xml/>
216 </assert_contents> 236 </assert_contents>
217 </output> 237 </output>
238 <assert_stdout>
239 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
240 </assert_stdout>
218 </test> 241 </test>
219 <!-- TOPP_FileConverter_5 --> 242 <!-- TOPP_FileConverter_5 -->
220 <test expect_num_outputs="2"> 243 <test expect_num_outputs="2">
221 <section name="adv_opts"> 244 <section name="adv_opts">
222 <param name="UID_postprocessing" value="ensure"/> 245 <param name="UID_postprocessing" value="ensure"/>
229 <param name="write_scan_index" value="true"/> 252 <param name="write_scan_index" value="true"/>
230 <param name="lossy_compression" value="false"/> 253 <param name="lossy_compression" value="false"/>
231 <param name="lossy_mass_accuracy" value="-1.0"/> 254 <param name="lossy_mass_accuracy" value="-1.0"/>
232 <param name="process_lowmemory" value="false"/> 255 <param name="process_lowmemory" value="false"/>
233 <param name="no_peak_picking" value="false"/> 256 <param name="no_peak_picking" value="false"/>
257 <param name="no_zlib_compression" value="false"/>
258 <param name="include_noise" value="false"/>
234 <param name="force" value="false"/> 259 <param name="force" value="false"/>
235 <param name="test" value="true"/> 260 <param name="test" value="true"/>
236 </section> 261 </section>
237 <param name="in" value="FileConverter_5_input.mzML"/> 262 <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"/> 263 <output name="out" value="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
239 <param name="out_type" value="mzXML"/> 264 <param name="out_type" value="mzXML"/>
240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 265 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
241 <output name="ctd_out" ftype="xml"> 266 <output name="ctd_out" ftype="xml">
242 <assert_contents> 267 <assert_contents>
243 <is_valid_xml/> 268 <is_valid_xml/>
244 </assert_contents> 269 </assert_contents>
245 </output> 270 </output>
271 <assert_stdout>
272 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
273 </assert_stdout>
246 </test> 274 </test>
247 <!-- TOPP_FileConverter_6 --> 275 <!-- TOPP_FileConverter_6 -->
248 <test expect_num_outputs="2"> 276 <test expect_num_outputs="2">
249 <section name="adv_opts"> 277 <section name="adv_opts">
250 <param name="UID_postprocessing" value="ensure"/> 278 <param name="UID_postprocessing" value="ensure"/>
257 <param name="write_scan_index" value="true"/> 285 <param name="write_scan_index" value="true"/>
258 <param name="lossy_compression" value="false"/> 286 <param name="lossy_compression" value="false"/>
259 <param name="lossy_mass_accuracy" value="-1.0"/> 287 <param name="lossy_mass_accuracy" value="-1.0"/>
260 <param name="process_lowmemory" value="false"/> 288 <param name="process_lowmemory" value="false"/>
261 <param name="no_peak_picking" value="false"/> 289 <param name="no_peak_picking" value="false"/>
290 <param name="no_zlib_compression" value="false"/>
291 <param name="include_noise" value="false"/>
262 <param name="force" value="false"/> 292 <param name="force" value="false"/>
263 <param name="test" value="true"/> 293 <param name="test" value="true"/>
264 </section> 294 </section>
265 <param name="in" value="FileConverter_6_input.mzML"/> 295 <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"/> 296 <output name="out" value="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
267 <param name="out_type" value="mzXML"/> 297 <param name="out_type" value="mzXML"/>
268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 298 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
269 <output name="ctd_out" ftype="xml"> 299 <output name="ctd_out" ftype="xml">
270 <assert_contents> 300 <assert_contents>
271 <is_valid_xml/> 301 <is_valid_xml/>
272 </assert_contents> 302 </assert_contents>
273 </output> 303 </output>
304 <assert_stdout>
305 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
306 </assert_stdout>
274 </test> 307 </test>
275 <!-- TOPP_FileConverter_7 --> 308 <!-- TOPP_FileConverter_7 -->
276 <test expect_num_outputs="2"> 309 <test expect_num_outputs="2">
277 <section name="adv_opts"> 310 <section name="adv_opts">
278 <param name="UID_postprocessing" value="ensure"/> 311 <param name="UID_postprocessing" value="ensure"/>
285 <param name="write_scan_index" value="true"/> 318 <param name="write_scan_index" value="true"/>
286 <param name="lossy_compression" value="false"/> 319 <param name="lossy_compression" value="false"/>
287 <param name="lossy_mass_accuracy" value="-1.0"/> 320 <param name="lossy_mass_accuracy" value="-1.0"/>
288 <param name="process_lowmemory" value="false"/> 321 <param name="process_lowmemory" value="false"/>
289 <param name="no_peak_picking" value="false"/> 322 <param name="no_peak_picking" value="false"/>
323 <param name="no_zlib_compression" value="false"/>
324 <param name="include_noise" value="false"/>
290 <param name="force" value="false"/> 325 <param name="force" value="false"/>
291 <param name="test" value="true"/> 326 <param name="test" value="true"/>
292 </section> 327 </section>
293 <param name="in" value="FileConverter_7_input.consensusXML"/> 328 <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"/> 329 <output name="out" value="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
295 <param name="out_type" value="featureXML"/> 330 <param name="out_type" value="featureXML"/>
296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 331 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
297 <output name="ctd_out" ftype="xml"> 332 <output name="ctd_out" ftype="xml">
298 <assert_contents> 333 <assert_contents>
299 <is_valid_xml/> 334 <is_valid_xml/>
300 </assert_contents> 335 </assert_contents>
301 </output> 336 </output>
337 <assert_stdout>
338 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
339 </assert_stdout>
302 </test> 340 </test>
303 <!-- TOPP_FileConverter_8 --> 341 <!-- TOPP_FileConverter_8 -->
304 <test expect_num_outputs="2"> 342 <test expect_num_outputs="2">
305 <section name="adv_opts"> 343 <section name="adv_opts">
306 <param name="UID_postprocessing" value="ensure"/> 344 <param name="UID_postprocessing" value="ensure"/>
313 <param name="write_scan_index" value="true"/> 351 <param name="write_scan_index" value="true"/>
314 <param name="lossy_compression" value="false"/> 352 <param name="lossy_compression" value="false"/>
315 <param name="lossy_mass_accuracy" value="-1.0"/> 353 <param name="lossy_mass_accuracy" value="-1.0"/>
316 <param name="process_lowmemory" value="false"/> 354 <param name="process_lowmemory" value="false"/>
317 <param name="no_peak_picking" value="false"/> 355 <param name="no_peak_picking" value="false"/>
356 <param name="no_zlib_compression" value="false"/>
357 <param name="include_noise" value="false"/>
318 <param name="force" value="false"/> 358 <param name="force" value="false"/>
319 <param name="test" value="true"/> 359 <param name="test" value="true"/>
320 </section> 360 </section>
321 <param name="in" value="FileConverter_8_input.mzML"/> 361 <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"/> 362 <output name="out" value="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
323 <param name="out_type" value="mzData"/> 363 <param name="out_type" value="mzData"/>
324 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 364 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
325 <output name="ctd_out" ftype="xml"> 365 <output name="ctd_out" ftype="xml">
326 <assert_contents> 366 <assert_contents>
327 <is_valid_xml/> 367 <is_valid_xml/>
328 </assert_contents> 368 </assert_contents>
329 </output> 369 </output>
370 <assert_stdout>
371 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
372 </assert_stdout>
330 </test> 373 </test>
331 <!-- TOPP_FileConverter_9 --> 374 <!-- TOPP_FileConverter_9 -->
332 <test expect_num_outputs="2"> 375 <test expect_num_outputs="2">
333 <section name="adv_opts"> 376 <section name="adv_opts">
334 <param name="UID_postprocessing" value="ensure"/> 377 <param name="UID_postprocessing" value="ensure"/>
341 <param name="write_scan_index" value="true"/> 384 <param name="write_scan_index" value="true"/>
342 <param name="lossy_compression" value="false"/> 385 <param name="lossy_compression" value="false"/>
343 <param name="lossy_mass_accuracy" value="-1.0"/> 386 <param name="lossy_mass_accuracy" value="-1.0"/>
344 <param name="process_lowmemory" value="false"/> 387 <param name="process_lowmemory" value="false"/>
345 <param name="no_peak_picking" value="false"/> 388 <param name="no_peak_picking" value="false"/>
389 <param name="no_zlib_compression" value="false"/>
390 <param name="include_noise" value="false"/>
346 <param name="force" value="false"/> 391 <param name="force" value="false"/>
347 <param name="test" value="true"/> 392 <param name="test" value="true"/>
348 </section> 393 </section>
349 <param name="in" value="FileConverter_9_input.consensusXML"/> 394 <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"/> 395 <output name="out" value="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
351 <param name="out_type" value="featureXML"/> 396 <param name="out_type" value="featureXML"/>
352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 397 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
353 <output name="ctd_out" ftype="xml"> 398 <output name="ctd_out" ftype="xml">
354 <assert_contents> 399 <assert_contents>
355 <is_valid_xml/> 400 <is_valid_xml/>
356 </assert_contents> 401 </assert_contents>
357 </output> 402 </output>
403 <assert_stdout>
404 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
405 </assert_stdout>
358 </test> 406 </test>
359 <!-- TOPP_FileConverter_10 --> 407 <!-- TOPP_FileConverter_10 -->
360 <test expect_num_outputs="2"> 408 <test expect_num_outputs="2">
361 <section name="adv_opts"> 409 <section name="adv_opts">
362 <param name="UID_postprocessing" value="ensure"/> 410 <param name="UID_postprocessing" value="ensure"/>
369 <param name="write_scan_index" value="true"/> 417 <param name="write_scan_index" value="true"/>
370 <param name="lossy_compression" value="false"/> 418 <param name="lossy_compression" value="false"/>
371 <param name="lossy_mass_accuracy" value="-1.0"/> 419 <param name="lossy_mass_accuracy" value="-1.0"/>
372 <param name="process_lowmemory" value="false"/> 420 <param name="process_lowmemory" value="false"/>
373 <param name="no_peak_picking" value="false"/> 421 <param name="no_peak_picking" value="false"/>
422 <param name="no_zlib_compression" value="false"/>
423 <param name="include_noise" value="false"/>
374 <param name="force" value="false"/> 424 <param name="force" value="false"/>
375 <param name="test" value="true"/> 425 <param name="test" value="true"/>
376 </section> 426 </section>
377 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> 427 <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"/> 428 <output name="out" value="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
379 <param name="out_type" value="featureXML"/> 429 <param name="out_type" value="featureXML"/>
380 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 430 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
381 <output name="ctd_out" ftype="xml"> 431 <output name="ctd_out" ftype="xml">
382 <assert_contents> 432 <assert_contents>
383 <is_valid_xml/> 433 <is_valid_xml/>
384 </assert_contents> 434 </assert_contents>
385 </output> 435 </output>
436 <assert_stdout>
437 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
438 </assert_stdout>
386 </test> 439 </test>
387 <!-- TOPP_FileConverter_11 --> 440 <!-- TOPP_FileConverter_11 -->
388 <test expect_num_outputs="2"> 441 <test expect_num_outputs="2">
389 <section name="adv_opts"> 442 <section name="adv_opts">
390 <param name="UID_postprocessing" value="ensure"/> 443 <param name="UID_postprocessing" value="ensure"/>
397 <param name="write_scan_index" value="true"/> 450 <param name="write_scan_index" value="true"/>
398 <param name="lossy_compression" value="false"/> 451 <param name="lossy_compression" value="false"/>
399 <param name="lossy_mass_accuracy" value="-1.0"/> 452 <param name="lossy_mass_accuracy" value="-1.0"/>
400 <param name="process_lowmemory" value="false"/> 453 <param name="process_lowmemory" value="false"/>
401 <param name="no_peak_picking" value="false"/> 454 <param name="no_peak_picking" value="false"/>
455 <param name="no_zlib_compression" value="false"/>
456 <param name="include_noise" value="false"/>
402 <param name="force" value="false"/> 457 <param name="force" value="false"/>
403 <param name="test" value="true"/> 458 <param name="test" value="true"/>
404 </section> 459 </section>
405 <param name="in" value="FileConverter_11_input.peplist"/> 460 <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"/> 461 <output name="out" value="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
407 <param name="out_type" value="featureXML"/> 462 <param name="out_type" value="featureXML"/>
408 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 463 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
409 <output name="ctd_out" ftype="xml"> 464 <output name="ctd_out" ftype="xml">
410 <assert_contents> 465 <assert_contents>
411 <is_valid_xml/> 466 <is_valid_xml/>
412 </assert_contents> 467 </assert_contents>
413 </output> 468 </output>
469 <assert_stdout>
470 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
471 </assert_stdout>
414 </test> 472 </test>
415 <!-- TOPP_FileConverter_12 --> 473 <!-- TOPP_FileConverter_12 -->
416 <test expect_num_outputs="2"> 474 <test expect_num_outputs="2">
417 <section name="adv_opts"> 475 <section name="adv_opts">
418 <param name="UID_postprocessing" value="ensure"/> 476 <param name="UID_postprocessing" value="ensure"/>
425 <param name="write_scan_index" value="true"/> 483 <param name="write_scan_index" value="true"/>
426 <param name="lossy_compression" value="false"/> 484 <param name="lossy_compression" value="false"/>
427 <param name="lossy_mass_accuracy" value="-1.0"/> 485 <param name="lossy_mass_accuracy" value="-1.0"/>
428 <param name="process_lowmemory" value="false"/> 486 <param name="process_lowmemory" value="false"/>
429 <param name="no_peak_picking" value="false"/> 487 <param name="no_peak_picking" value="false"/>
488 <param name="no_zlib_compression" value="false"/>
489 <param name="include_noise" value="false"/>
430 <param name="force" value="false"/> 490 <param name="force" value="false"/>
431 <param name="test" value="true"/> 491 <param name="test" value="true"/>
432 </section> 492 </section>
433 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> 493 <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"/> 494 <output name="out" value="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
435 <param name="out_type" value="featureXML"/> 495 <param name="out_type" value="featureXML"/>
436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 496 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
437 <output name="ctd_out" ftype="xml"> 497 <output name="ctd_out" ftype="xml">
438 <assert_contents> 498 <assert_contents>
439 <is_valid_xml/> 499 <is_valid_xml/>
440 </assert_contents> 500 </assert_contents>
441 </output> 501 </output>
502 <assert_stdout>
503 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
504 </assert_stdout>
442 </test> 505 </test>
443 <!-- TOPP_FileConverter_13 --> 506 <!-- TOPP_FileConverter_13 -->
444 <test expect_num_outputs="2"> 507 <test expect_num_outputs="2">
445 <section name="adv_opts"> 508 <section name="adv_opts">
446 <param name="UID_postprocessing" value="ensure"/> 509 <param name="UID_postprocessing" value="ensure"/>
453 <param name="write_scan_index" value="true"/> 516 <param name="write_scan_index" value="true"/>
454 <param name="lossy_compression" value="false"/> 517 <param name="lossy_compression" value="false"/>
455 <param name="lossy_mass_accuracy" value="-1.0"/> 518 <param name="lossy_mass_accuracy" value="-1.0"/>
456 <param name="process_lowmemory" value="false"/> 519 <param name="process_lowmemory" value="false"/>
457 <param name="no_peak_picking" value="false"/> 520 <param name="no_peak_picking" value="false"/>
521 <param name="no_zlib_compression" value="false"/>
522 <param name="include_noise" value="false"/>
458 <param name="force" value="false"/> 523 <param name="force" value="false"/>
459 <param name="test" value="true"/> 524 <param name="test" value="true"/>
460 </section> 525 </section>
461 <param name="in" value="FileConverter_13_input.peptides.kroenik"/> 526 <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"/> 527 <output name="out" value="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
463 <param name="out_type" value="featureXML"/> 528 <param name="out_type" value="featureXML"/>
464 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 529 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
465 <output name="ctd_out" ftype="xml"> 530 <output name="ctd_out" ftype="xml">
466 <assert_contents> 531 <assert_contents>
467 <is_valid_xml/> 532 <is_valid_xml/>
468 </assert_contents> 533 </assert_contents>
469 </output> 534 </output>
535 <assert_stdout>
536 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
537 </assert_stdout>
470 </test> 538 </test>
471 <!-- TOPP_FileConverter_14 --> 539 <!-- TOPP_FileConverter_14 -->
472 <test expect_num_outputs="2"> 540 <test expect_num_outputs="2">
473 <section name="adv_opts"> 541 <section name="adv_opts">
474 <param name="UID_postprocessing" value="ensure"/> 542 <param name="UID_postprocessing" value="ensure"/>
481 <param name="write_scan_index" value="true"/> 549 <param name="write_scan_index" value="true"/>
482 <param name="lossy_compression" value="false"/> 550 <param name="lossy_compression" value="false"/>
483 <param name="lossy_mass_accuracy" value="-1.0"/> 551 <param name="lossy_mass_accuracy" value="-1.0"/>
484 <param name="process_lowmemory" value="false"/> 552 <param name="process_lowmemory" value="false"/>
485 <param name="no_peak_picking" value="false"/> 553 <param name="no_peak_picking" value="false"/>
554 <param name="no_zlib_compression" value="false"/>
555 <param name="include_noise" value="false"/>
486 <param name="force" value="false"/> 556 <param name="force" value="false"/>
487 <param name="test" value="true"/> 557 <param name="test" value="true"/>
488 </section> 558 </section>
489 <param name="in" value="FileConverter_9_output.featureXML"/> 559 <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"/> 560 <output name="out" value="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
491 <param name="out_type" value="consensusXML"/> 561 <param name="out_type" value="consensusXML"/>
492 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 562 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
493 <output name="ctd_out" ftype="xml"> 563 <output name="ctd_out" ftype="xml">
494 <assert_contents> 564 <assert_contents>
495 <is_valid_xml/> 565 <is_valid_xml/>
496 </assert_contents> 566 </assert_contents>
497 </output> 567 </output>
568 <assert_stdout>
569 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
570 </assert_stdout>
498 </test> 571 </test>
499 <!-- TOPP_FileConverter_15 --> 572 <!-- TOPP_FileConverter_15 -->
500 <test expect_num_outputs="2"> 573 <test expect_num_outputs="2">
501 <section name="adv_opts"> 574 <section name="adv_opts">
502 <param name="UID_postprocessing" value="ensure"/> 575 <param name="UID_postprocessing" value="ensure"/>
509 <param name="write_scan_index" value="true"/> 582 <param name="write_scan_index" value="true"/>
510 <param name="lossy_compression" value="false"/> 583 <param name="lossy_compression" value="false"/>
511 <param name="lossy_mass_accuracy" value="-1.0"/> 584 <param name="lossy_mass_accuracy" value="-1.0"/>
512 <param name="process_lowmemory" value="false"/> 585 <param name="process_lowmemory" value="false"/>
513 <param name="no_peak_picking" value="false"/> 586 <param name="no_peak_picking" value="false"/>
587 <param name="no_zlib_compression" value="false"/>
588 <param name="include_noise" value="false"/>
514 <param name="force" value="false"/> 589 <param name="force" value="false"/>
515 <param name="test" value="true"/> 590 <param name="test" value="true"/>
516 </section> 591 </section>
517 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> 592 <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"/> 593 <output name="out" value="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
519 <param name="out_type" value="consensusXML"/> 594 <param name="out_type" value="consensusXML"/>
520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
521 <output name="ctd_out" ftype="xml"> 596 <output name="ctd_out" ftype="xml">
522 <assert_contents> 597 <assert_contents>
523 <is_valid_xml/> 598 <is_valid_xml/>
524 </assert_contents> 599 </assert_contents>
525 </output> 600 </output>
601 <assert_stdout>
602 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
603 </assert_stdout>
526 </test> 604 </test>
527 <!-- TOPP_FileConverter_16 --> 605 <!-- TOPP_FileConverter_16 -->
528 <test expect_num_outputs="2"> 606 <test expect_num_outputs="2">
529 <section name="adv_opts"> 607 <section name="adv_opts">
530 <param name="UID_postprocessing" value="ensure"/> 608 <param name="UID_postprocessing" value="ensure"/>
537 <param name="write_scan_index" value="true"/> 615 <param name="write_scan_index" value="true"/>
538 <param name="lossy_compression" value="false"/> 616 <param name="lossy_compression" value="false"/>
539 <param name="lossy_mass_accuracy" value="-1.0"/> 617 <param name="lossy_mass_accuracy" value="-1.0"/>
540 <param name="process_lowmemory" value="false"/> 618 <param name="process_lowmemory" value="false"/>
541 <param name="no_peak_picking" value="false"/> 619 <param name="no_peak_picking" value="false"/>
620 <param name="no_zlib_compression" value="false"/>
621 <param name="include_noise" value="false"/>
542 <param name="force" value="false"/> 622 <param name="force" value="false"/>
543 <param name="test" value="true"/> 623 <param name="test" value="true"/>
544 </section> 624 </section>
545 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> 625 <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"/> 626 <output name="out" value="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
547 <param name="out_type" value="consensusXML"/> 627 <param name="out_type" value="consensusXML"/>
548 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 628 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
549 <output name="ctd_out" ftype="xml"> 629 <output name="ctd_out" ftype="xml">
550 <assert_contents> 630 <assert_contents>
551 <is_valid_xml/> 631 <is_valid_xml/>
552 </assert_contents> 632 </assert_contents>
553 </output> 633 </output>
634 <assert_stdout>
635 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
636 </assert_stdout>
554 </test> 637 </test>
555 <!-- TOPP_FileConverter_17 --> 638 <!-- TOPP_FileConverter_17 -->
556 <test expect_num_outputs="2"> 639 <test expect_num_outputs="2">
557 <section name="adv_opts"> 640 <section name="adv_opts">
558 <param name="UID_postprocessing" value="ensure"/> 641 <param name="UID_postprocessing" value="ensure"/>
565 <param name="write_scan_index" value="true"/> 648 <param name="write_scan_index" value="true"/>
566 <param name="lossy_compression" value="false"/> 649 <param name="lossy_compression" value="false"/>
567 <param name="lossy_mass_accuracy" value="-1.0"/> 650 <param name="lossy_mass_accuracy" value="-1.0"/>
568 <param name="process_lowmemory" value="false"/> 651 <param name="process_lowmemory" value="false"/>
569 <param name="no_peak_picking" value="false"/> 652 <param name="no_peak_picking" value="false"/>
653 <param name="no_zlib_compression" value="false"/>
654 <param name="include_noise" value="false"/>
570 <param name="force" value="false"/> 655 <param name="force" value="false"/>
571 <param name="test" value="true"/> 656 <param name="test" value="true"/>
572 </section> 657 </section>
573 <param name="in" value="FileConverter_17_input.consensusXML"/> 658 <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"/> 659 <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
575 <param name="out_type" value="csv"/> 660 <param name="out_type" value="csv"/>
576 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 661 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
577 <output name="ctd_out" ftype="xml"> 662 <output name="ctd_out" ftype="xml">
578 <assert_contents> 663 <assert_contents>
579 <is_valid_xml/> 664 <is_valid_xml/>
580 </assert_contents> 665 </assert_contents>
581 </output> 666 </output>
667 <assert_stdout>
668 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
669 </assert_stdout>
582 </test> 670 </test>
583 <!-- TOPP_FileConverter_18 --> 671 <!-- TOPP_FileConverter_18 -->
584 <test expect_num_outputs="2"> 672 <test expect_num_outputs="2">
585 <section name="adv_opts"> 673 <section name="adv_opts">
586 <param name="UID_postprocessing" value="ensure"/> 674 <param name="UID_postprocessing" value="ensure"/>
593 <param name="write_scan_index" value="true"/> 681 <param name="write_scan_index" value="true"/>
594 <param name="lossy_compression" value="false"/> 682 <param name="lossy_compression" value="false"/>
595 <param name="lossy_mass_accuracy" value="-1.0"/> 683 <param name="lossy_mass_accuracy" value="-1.0"/>
596 <param name="process_lowmemory" value="false"/> 684 <param name="process_lowmemory" value="false"/>
597 <param name="no_peak_picking" value="false"/> 685 <param name="no_peak_picking" value="false"/>
686 <param name="no_zlib_compression" value="false"/>
687 <param name="include_noise" value="false"/>
598 <param name="force" value="false"/> 688 <param name="force" value="false"/>
599 <param name="test" value="true"/> 689 <param name="test" value="true"/>
600 </section> 690 </section>
601 <param name="in" value="FileConverter_17_input.consensusXML"/> 691 <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"/> 692 <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
603 <param name="out_type" value="csv"/> 693 <param name="out_type" value="csv"/>
604 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 694 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
605 <output name="ctd_out" ftype="xml"> 695 <output name="ctd_out" ftype="xml">
606 <assert_contents> 696 <assert_contents>
607 <is_valid_xml/> 697 <is_valid_xml/>
608 </assert_contents> 698 </assert_contents>
609 </output> 699 </output>
700 <assert_stdout>
701 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
702 </assert_stdout>
610 </test> 703 </test>
611 <!-- TOPP_FileConverter_19 --> 704 <!-- TOPP_FileConverter_19 -->
612 <test expect_num_outputs="2"> 705 <test expect_num_outputs="2">
613 <section name="adv_opts"> 706 <section name="adv_opts">
614 <param name="UID_postprocessing" value="ensure"/> 707 <param name="UID_postprocessing" value="ensure"/>
621 <param name="write_scan_index" value="true"/> 714 <param name="write_scan_index" value="true"/>
622 <param name="lossy_compression" value="false"/> 715 <param name="lossy_compression" value="false"/>
623 <param name="lossy_mass_accuracy" value="-1.0"/> 716 <param name="lossy_mass_accuracy" value="-1.0"/>
624 <param name="process_lowmemory" value="true"/> 717 <param name="process_lowmemory" value="true"/>
625 <param name="no_peak_picking" value="false"/> 718 <param name="no_peak_picking" value="false"/>
719 <param name="no_zlib_compression" value="false"/>
720 <param name="include_noise" value="false"/>
626 <param name="force" value="false"/> 721 <param name="force" value="false"/>
627 <param name="test" value="true"/> 722 <param name="test" value="true"/>
628 </section> 723 </section>
629 <param name="in" value="FileFilter_1_input.mzML"/> 724 <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"/> 725 <output name="out" value="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
631 <param name="out_type" value="mzML"/> 726 <param name="out_type" value="mzML"/>
632 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
633 <output name="ctd_out" ftype="xml"> 728 <output name="ctd_out" ftype="xml">
634 <assert_contents> 729 <assert_contents>
635 <is_valid_xml/> 730 <is_valid_xml/>
636 </assert_contents> 731 </assert_contents>
637 </output> 732 </output>
733 <assert_stdout>
734 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
735 </assert_stdout>
638 </test> 736 </test>
639 <!-- TOPP_FileConverter_20 --> 737 <!-- TOPP_FileConverter_20 -->
640 <test expect_num_outputs="2"> 738 <test expect_num_outputs="2">
641 <section name="adv_opts"> 739 <section name="adv_opts">
642 <param name="UID_postprocessing" value="ensure"/> 740 <param name="UID_postprocessing" value="ensure"/>
649 <param name="write_scan_index" value="true"/> 747 <param name="write_scan_index" value="true"/>
650 <param name="lossy_compression" value="false"/> 748 <param name="lossy_compression" value="false"/>
651 <param name="lossy_mass_accuracy" value="-1.0"/> 749 <param name="lossy_mass_accuracy" value="-1.0"/>
652 <param name="process_lowmemory" value="false"/> 750 <param name="process_lowmemory" value="false"/>
653 <param name="no_peak_picking" value="false"/> 751 <param name="no_peak_picking" value="false"/>
752 <param name="no_zlib_compression" value="false"/>
753 <param name="include_noise" value="false"/>
654 <param name="force" value="false"/> 754 <param name="force" value="false"/>
655 <param name="test" value="true"/> 755 <param name="test" value="true"/>
656 </section> 756 </section>
657 <param name="in" value="FileConverter_20_input.featureXML"/> 757 <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"/> 758 <output name="out" value="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
659 <param name="out_type" value="featureXML"/> 759 <param name="out_type" value="featureXML"/>
660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 760 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
661 <output name="ctd_out" ftype="xml"> 761 <output name="ctd_out" ftype="xml">
662 <assert_contents> 762 <assert_contents>
663 <is_valid_xml/> 763 <is_valid_xml/>
664 </assert_contents> 764 </assert_contents>
665 </output> 765 </output>
766 <assert_stdout>
767 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
768 </assert_stdout>
666 </test> 769 </test>
667 <!-- TOPP_FileConverter_21 --> 770 <!-- TOPP_FileConverter_21 -->
668 <test expect_num_outputs="2"> 771 <test expect_num_outputs="2">
669 <section name="adv_opts"> 772 <section name="adv_opts">
670 <param name="UID_postprocessing" value="ensure"/> 773 <param name="UID_postprocessing" value="ensure"/>
677 <param name="write_scan_index" value="true"/> 780 <param name="write_scan_index" value="true"/>
678 <param name="lossy_compression" value="false"/> 781 <param name="lossy_compression" value="false"/>
679 <param name="lossy_mass_accuracy" value="-1.0"/> 782 <param name="lossy_mass_accuracy" value="-1.0"/>
680 <param name="process_lowmemory" value="true"/> 783 <param name="process_lowmemory" value="true"/>
681 <param name="no_peak_picking" value="false"/> 784 <param name="no_peak_picking" value="false"/>
785 <param name="no_zlib_compression" value="false"/>
786 <param name="include_noise" value="false"/>
682 <param name="force" value="false"/> 787 <param name="force" value="false"/>
683 <param name="test" value="true"/> 788 <param name="test" value="true"/>
684 </section> 789 </section>
685 <param name="in" value="FileConverter_4_input.mzXML"/> 790 <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"/> 791 <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
687 <param name="out_type" value="mzML"/> 792 <param name="out_type" value="mzML"/>
688 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 793 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
689 <output name="ctd_out" ftype="xml"> 794 <output name="ctd_out" ftype="xml">
690 <assert_contents> 795 <assert_contents>
691 <is_valid_xml/> 796 <is_valid_xml/>
692 </assert_contents> 797 </assert_contents>
693 </output> 798 </output>
799 <assert_stdout>
800 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
801 </assert_stdout>
694 </test> 802 </test>
695 <!-- TOPP_FileConverter_23 --> 803 <!-- TOPP_FileConverter_23 -->
696 <test expect_num_outputs="2"> 804 <test expect_num_outputs="2">
697 <section name="adv_opts"> 805 <section name="adv_opts">
698 <param name="UID_postprocessing" value="ensure"/> 806 <param name="UID_postprocessing" value="ensure"/>
705 <param name="write_scan_index" value="true"/> 813 <param name="write_scan_index" value="true"/>
706 <param name="lossy_compression" value="false"/> 814 <param name="lossy_compression" value="false"/>
707 <param name="lossy_mass_accuracy" value="-1.0"/> 815 <param name="lossy_mass_accuracy" value="-1.0"/>
708 <param name="process_lowmemory" value="false"/> 816 <param name="process_lowmemory" value="false"/>
709 <param name="no_peak_picking" value="false"/> 817 <param name="no_peak_picking" value="false"/>
818 <param name="no_zlib_compression" value="false"/>
819 <param name="include_noise" value="false"/>
710 <param name="force" value="false"/> 820 <param name="force" value="false"/>
711 <param name="test" value="true"/> 821 <param name="test" value="true"/>
712 </section> 822 </section>
713 <param name="in" value="FileConverter_23_input.mzML"/> 823 <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"/> 824 <output name="out" value="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
715 <param name="out_type" value="mzML"/> 825 <param name="out_type" value="mzML"/>
716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 826 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
717 <output name="ctd_out" ftype="xml"> 827 <output name="ctd_out" ftype="xml">
718 <assert_contents> 828 <assert_contents>
719 <is_valid_xml/> 829 <is_valid_xml/>
720 </assert_contents> 830 </assert_contents>
721 </output> 831 </output>
832 <assert_stdout>
833 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
834 </assert_stdout>
722 </test> 835 </test>
723 <!-- TOPP_FileConverter_24 --> 836 <!-- TOPP_FileConverter_24 -->
724 <test expect_num_outputs="2"> 837 <test expect_num_outputs="2">
725 <section name="adv_opts"> 838 <section name="adv_opts">
726 <param name="UID_postprocessing" value="ensure"/> 839 <param name="UID_postprocessing" value="ensure"/>
733 <param name="write_scan_index" value="true"/> 846 <param name="write_scan_index" value="true"/>
734 <param name="lossy_compression" value="true"/> 847 <param name="lossy_compression" value="true"/>
735 <param name="lossy_mass_accuracy" value="0.0001"/> 848 <param name="lossy_mass_accuracy" value="0.0001"/>
736 <param name="process_lowmemory" value="true"/> 849 <param name="process_lowmemory" value="true"/>
737 <param name="no_peak_picking" value="false"/> 850 <param name="no_peak_picking" value="false"/>
851 <param name="no_zlib_compression" value="false"/>
852 <param name="include_noise" value="false"/>
738 <param name="force" value="false"/> 853 <param name="force" value="false"/>
739 <param name="test" value="true"/> 854 <param name="test" value="true"/>
740 </section> 855 </section>
741 <param name="in" value="FileFilter_1_input.mzML"/> 856 <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"/> 857 <output name="out" value="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
743 <param name="out_type" value="mzML"/> 858 <param name="out_type" value="mzML"/>
744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 859 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
745 <output name="ctd_out" ftype="xml"> 860 <output name="ctd_out" ftype="xml">
746 <assert_contents> 861 <assert_contents>
747 <is_valid_xml/> 862 <is_valid_xml/>
748 </assert_contents> 863 </assert_contents>
749 </output> 864 </output>
865 <assert_stdout>
866 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
867 </assert_stdout>
750 </test> 868 </test>
751 <!-- TOPP_FileConverter_25 --> 869 <!-- TOPP_FileConverter_25 -->
752 <test expect_num_outputs="2"> 870 <test expect_num_outputs="2">
753 <section name="adv_opts"> 871 <section name="adv_opts">
754 <param name="UID_postprocessing" value="ensure"/> 872 <param name="UID_postprocessing" value="ensure"/>
761 <param name="write_scan_index" value="true"/> 879 <param name="write_scan_index" value="true"/>
762 <param name="lossy_compression" value="true"/> 880 <param name="lossy_compression" value="true"/>
763 <param name="lossy_mass_accuracy" value="-1.0"/> 881 <param name="lossy_mass_accuracy" value="-1.0"/>
764 <param name="process_lowmemory" value="true"/> 882 <param name="process_lowmemory" value="true"/>
765 <param name="no_peak_picking" value="false"/> 883 <param name="no_peak_picking" value="false"/>
884 <param name="no_zlib_compression" value="false"/>
885 <param name="include_noise" value="false"/>
766 <param name="force" value="false"/> 886 <param name="force" value="false"/>
767 <param name="test" value="true"/> 887 <param name="test" value="true"/>
768 </section> 888 </section>
769 <param name="in" value="FileFilter_1_input.mzML"/> 889 <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"/> 890 <output name="out" value="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
771 <param name="out_type" value="mzML"/> 891 <param name="out_type" value="mzML"/>
772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 892 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
773 <output name="ctd_out" ftype="xml"> 893 <output name="ctd_out" ftype="xml">
774 <assert_contents> 894 <assert_contents>
775 <is_valid_xml/> 895 <is_valid_xml/>
776 </assert_contents> 896 </assert_contents>
777 </output> 897 </output>
898 <assert_stdout>
899 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
900 </assert_stdout>
778 </test> 901 </test>
779 <!-- TOPP_FileConverter_26 --> 902 <!-- TOPP_FileConverter_26 -->
780 <test expect_num_outputs="2"> 903 <test expect_num_outputs="2">
781 <section name="adv_opts"> 904 <section name="adv_opts">
782 <param name="UID_postprocessing" value="ensure"/> 905 <param name="UID_postprocessing" value="ensure"/>
789 <param name="write_scan_index" value="true"/> 912 <param name="write_scan_index" value="true"/>
790 <param name="lossy_compression" value="false"/> 913 <param name="lossy_compression" value="false"/>
791 <param name="lossy_mass_accuracy" value="-1.0"/> 914 <param name="lossy_mass_accuracy" value="-1.0"/>
792 <param name="process_lowmemory" value="false"/> 915 <param name="process_lowmemory" value="false"/>
793 <param name="no_peak_picking" value="false"/> 916 <param name="no_peak_picking" value="false"/>
917 <param name="no_zlib_compression" value="false"/>
918 <param name="include_noise" value="false"/>
794 <param name="force" value="false"/> 919 <param name="force" value="false"/>
795 <param name="test" value="true"/> 920 <param name="test" value="true"/>
796 </section> 921 </section>
797 <param name="in" value="FileFilter_1_input.mzML"/> 922 <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"/> 923 <output name="out" value="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
799 <param name="out_type" value="mzXML"/> 924 <param name="out_type" value="mzXML"/>
800 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 925 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
801 <output name="ctd_out" ftype="xml"> 926 <output name="ctd_out" ftype="xml">
802 <assert_contents> 927 <assert_contents>
803 <is_valid_xml/> 928 <is_valid_xml/>
804 </assert_contents> 929 </assert_contents>
805 </output> 930 </output>
931 <assert_stdout>
932 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
933 </assert_stdout>
806 </test> 934 </test>
807 <!-- TOPP_FileConverter_26-2 --> 935 <!-- TOPP_FileConverter_26-2 -->
808 <test expect_num_outputs="2"> 936 <test expect_num_outputs="2">
809 <section name="adv_opts"> 937 <section name="adv_opts">
810 <param name="UID_postprocessing" value="ensure"/> 938 <param name="UID_postprocessing" value="ensure"/>
817 <param name="write_scan_index" value="true"/> 945 <param name="write_scan_index" value="true"/>
818 <param name="lossy_compression" value="false"/> 946 <param name="lossy_compression" value="false"/>
819 <param name="lossy_mass_accuracy" value="-1.0"/> 947 <param name="lossy_mass_accuracy" value="-1.0"/>
820 <param name="process_lowmemory" value="false"/> 948 <param name="process_lowmemory" value="false"/>
821 <param name="no_peak_picking" value="false"/> 949 <param name="no_peak_picking" value="false"/>
950 <param name="no_zlib_compression" value="false"/>
951 <param name="include_noise" value="false"/>
822 <param name="force" value="false"/> 952 <param name="force" value="false"/>
823 <param name="test" value="true"/> 953 <param name="test" value="true"/>
824 </section> 954 </section>
825 <param name="in" value="FileConverter_26_output.mzXML"/> 955 <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"/> 956 <output name="out" value="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
827 <param name="out_type" value="mzXML"/> 957 <param name="out_type" value="mzXML"/>
828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 958 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
829 <output name="ctd_out" ftype="xml"> 959 <output name="ctd_out" ftype="xml">
830 <assert_contents> 960 <assert_contents>
831 <is_valid_xml/> 961 <is_valid_xml/>
832 </assert_contents> 962 </assert_contents>
833 </output> 963 </output>
964 <assert_stdout>
965 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
966 </assert_stdout>
834 </test> 967 </test>
835 <!-- TOPP_FileConverter_27 --> 968 <!-- TOPP_FileConverter_27 -->
836 <test expect_num_outputs="2"> 969 <test expect_num_outputs="2">
837 <section name="adv_opts"> 970 <section name="adv_opts">
838 <param name="UID_postprocessing" value="ensure"/> 971 <param name="UID_postprocessing" value="ensure"/>
845 <param name="write_scan_index" value="true"/> 978 <param name="write_scan_index" value="true"/>
846 <param name="lossy_compression" value="false"/> 979 <param name="lossy_compression" value="false"/>
847 <param name="lossy_mass_accuracy" value="-1.0"/> 980 <param name="lossy_mass_accuracy" value="-1.0"/>
848 <param name="process_lowmemory" value="false"/> 981 <param name="process_lowmemory" value="false"/>
849 <param name="no_peak_picking" value="false"/> 982 <param name="no_peak_picking" value="false"/>
983 <param name="no_zlib_compression" value="false"/>
984 <param name="include_noise" value="false"/>
850 <param name="force" value="false"/> 985 <param name="force" value="false"/>
851 <param name="test" value="true"/> 986 <param name="test" value="true"/>
852 </section> 987 </section>
853 <param name="in" value="FileConverter_27_input.mzML"/> 988 <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"/> 989 <output name="out" value="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
855 <param name="out_type" value="mzML"/> 990 <param name="out_type" value="mzML"/>
856 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 991 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
857 <output name="ctd_out" ftype="xml"> 992 <output name="ctd_out" ftype="xml">
858 <assert_contents> 993 <assert_contents>
859 <is_valid_xml/> 994 <is_valid_xml/>
860 </assert_contents> 995 </assert_contents>
861 </output> 996 </output>
997 <assert_stdout>
998 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
999 </assert_stdout>
862 </test> 1000 </test>
863 <!-- TOPP_FileConverter_28 --> 1001 <!-- TOPP_FileConverter_28 -->
864 <test expect_num_outputs="2"> 1002 <test expect_num_outputs="2">
865 <section name="adv_opts"> 1003 <section name="adv_opts">
866 <param name="UID_postprocessing" value="ensure"/> 1004 <param name="UID_postprocessing" value="ensure"/>
873 <param name="write_scan_index" value="true"/> 1011 <param name="write_scan_index" value="true"/>
874 <param name="lossy_compression" value="false"/> 1012 <param name="lossy_compression" value="false"/>
875 <param name="lossy_mass_accuracy" value="-1.0"/> 1013 <param name="lossy_mass_accuracy" value="-1.0"/>
876 <param name="process_lowmemory" value="false"/> 1014 <param name="process_lowmemory" value="false"/>
877 <param name="no_peak_picking" value="false"/> 1015 <param name="no_peak_picking" value="false"/>
1016 <param name="no_zlib_compression" value="false"/>
1017 <param name="include_noise" value="false"/>
878 <param name="force" value="false"/> 1018 <param name="force" value="false"/>
879 <param name="test" value="true"/> 1019 <param name="test" value="true"/>
880 </section> 1020 </section>
881 <param name="in" value="FileConverter_28_input.mzML"/> 1021 <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"/> 1022 <output name="out" value="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
883 <param name="out_type" value="mzML"/> 1023 <param name="out_type" value="mzML"/>
884 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1024 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
885 <output name="ctd_out" ftype="xml"> 1025 <output name="ctd_out" ftype="xml">
886 <assert_contents> 1026 <assert_contents>
887 <is_valid_xml/> 1027 <is_valid_xml/>
888 </assert_contents> 1028 </assert_contents>
889 </output> 1029 </output>
1030 <assert_stdout>
1031 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1032 </assert_stdout>
890 </test> 1033 </test>
891 <!-- TOPP_FileConverter_29 --> 1034 <!-- TOPP_FileConverter_29 -->
892 <test expect_num_outputs="2"> 1035 <test expect_num_outputs="2">
893 <section name="adv_opts"> 1036 <section name="adv_opts">
894 <param name="UID_postprocessing" value="ensure"/> 1037 <param name="UID_postprocessing" value="ensure"/>
901 <param name="write_scan_index" value="true"/> 1044 <param name="write_scan_index" value="true"/>
902 <param name="lossy_compression" value="true"/> 1045 <param name="lossy_compression" value="true"/>
903 <param name="lossy_mass_accuracy" value="1e-05"/> 1046 <param name="lossy_mass_accuracy" value="1e-05"/>
904 <param name="process_lowmemory" value="true"/> 1047 <param name="process_lowmemory" value="true"/>
905 <param name="no_peak_picking" value="false"/> 1048 <param name="no_peak_picking" value="false"/>
1049 <param name="no_zlib_compression" value="false"/>
1050 <param name="include_noise" value="false"/>
906 <param name="force" value="false"/> 1051 <param name="force" value="false"/>
907 <param name="test" value="true"/> 1052 <param name="test" value="true"/>
908 </section> 1053 </section>
909 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> 1054 <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"/> 1055 <output name="out" value="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
911 <param name="out_type" value="mzML"/> 1056 <param name="out_type" value="mzML"/>
912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1057 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
913 <output name="ctd_out" ftype="xml"> 1058 <output name="ctd_out" ftype="xml">
914 <assert_contents> 1059 <assert_contents>
915 <is_valid_xml/> 1060 <is_valid_xml/>
916 </assert_contents> 1061 </assert_contents>
917 </output> 1062 </output>
1063 <assert_stdout>
1064 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1065 </assert_stdout>
918 </test> 1066 </test>
919 <!-- TOPP_FileConverter_29_back --> 1067 <!-- TOPP_FileConverter_29_back -->
920 <test expect_num_outputs="2"> 1068 <test expect_num_outputs="2">
921 <section name="adv_opts"> 1069 <section name="adv_opts">
922 <param name="UID_postprocessing" value="ensure"/> 1070 <param name="UID_postprocessing" value="ensure"/>
929 <param name="write_scan_index" value="true"/> 1077 <param name="write_scan_index" value="true"/>
930 <param name="lossy_compression" value="false"/> 1078 <param name="lossy_compression" value="false"/>
931 <param name="lossy_mass_accuracy" value="-1.0"/> 1079 <param name="lossy_mass_accuracy" value="-1.0"/>
932 <param name="process_lowmemory" value="false"/> 1080 <param name="process_lowmemory" value="false"/>
933 <param name="no_peak_picking" value="false"/> 1081 <param name="no_peak_picking" value="false"/>
1082 <param name="no_zlib_compression" value="false"/>
1083 <param name="include_noise" value="false"/>
934 <param name="force" value="false"/> 1084 <param name="force" value="false"/>
935 <param name="test" value="true"/> 1085 <param name="test" value="true"/>
936 </section> 1086 </section>
937 <param name="in" value="FileConverter_29_output.mzML"/> 1087 <param name="in" value="FileConverter_29_output.mzML"/>
938 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/> 1088 <output name="out" value="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
939 <param name="out_type" value="mzML"/> 1089 <param name="out_type" value="mzML"/>
940 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1090 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
941 <output name="ctd_out" ftype="xml"> 1091 <output name="ctd_out" ftype="xml">
942 <assert_contents> 1092 <assert_contents>
943 <is_valid_xml/> 1093 <is_valid_xml/>
944 </assert_contents> 1094 </assert_contents>
945 </output> 1095 </output>
1096 <assert_stdout>
1097 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1098 </assert_stdout>
946 </test> 1099 </test>
947 <!-- TOPP_FileConverter_30 --> 1100 <!-- TOPP_FileConverter_30 -->
948 <test expect_num_outputs="2"> 1101 <test expect_num_outputs="2">
949 <section name="adv_opts"> 1102 <section name="adv_opts">
950 <param name="UID_postprocessing" value="ensure"/> 1103 <param name="UID_postprocessing" value="ensure"/>
957 <param name="write_scan_index" value="true"/> 1110 <param name="write_scan_index" value="true"/>
958 <param name="lossy_compression" value="false"/> 1111 <param name="lossy_compression" value="false"/>
959 <param name="lossy_mass_accuracy" value="-1.0"/> 1112 <param name="lossy_mass_accuracy" value="-1.0"/>
960 <param name="process_lowmemory" value="false"/> 1113 <param name="process_lowmemory" value="false"/>
961 <param name="no_peak_picking" value="false"/> 1114 <param name="no_peak_picking" value="false"/>
1115 <param name="no_zlib_compression" value="false"/>
1116 <param name="include_noise" value="false"/>
962 <param name="force" value="false"/> 1117 <param name="force" value="false"/>
963 <param name="test" value="true"/> 1118 <param name="test" value="true"/>
964 </section> 1119 </section>
965 <param name="in" value="FileConverter_30_input.mzML"/> 1120 <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"/> 1121 <output name="out" value="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
967 <param name="out_type" value="mzML"/> 1122 <param name="out_type" value="mzML"/>
968 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
969 <output name="ctd_out" ftype="xml"> 1124 <output name="ctd_out" ftype="xml">
970 <assert_contents> 1125 <assert_contents>
971 <is_valid_xml/> 1126 <is_valid_xml/>
972 </assert_contents> 1127 </assert_contents>
973 </output> 1128 </output>
1129 <assert_stdout>
1130 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1131 </assert_stdout>
974 </test> 1132 </test>
975 <!-- TOPP_FileConverter_31 --> 1133 <!-- TOPP_FileConverter_31 -->
976 <test expect_num_outputs="2"> 1134 <test expect_num_outputs="2">
977 <section name="adv_opts"> 1135 <section name="adv_opts">
978 <param name="UID_postprocessing" value="ensure"/> 1136 <param name="UID_postprocessing" value="ensure"/>
985 <param name="write_scan_index" value="true"/> 1143 <param name="write_scan_index" value="true"/>
986 <param name="lossy_compression" value="false"/> 1144 <param name="lossy_compression" value="false"/>
987 <param name="lossy_mass_accuracy" value="-1.0"/> 1145 <param name="lossy_mass_accuracy" value="-1.0"/>
988 <param name="process_lowmemory" value="false"/> 1146 <param name="process_lowmemory" value="false"/>
989 <param name="no_peak_picking" value="false"/> 1147 <param name="no_peak_picking" value="false"/>
1148 <param name="no_zlib_compression" value="false"/>
1149 <param name="include_noise" value="false"/>
990 <param name="force" value="false"/> 1150 <param name="force" value="false"/>
991 <param name="test" value="true"/> 1151 <param name="test" value="true"/>
992 </section> 1152 </section>
993 <param name="in" value="FileConverter_30_output.mzML"/> 1153 <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"/> 1154 <output name="out" value="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
995 <param name="out_type" value="mzML"/> 1155 <param name="out_type" value="mzML"/>
996 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
997 <output name="ctd_out" ftype="xml"> 1157 <output name="ctd_out" ftype="xml">
998 <assert_contents> 1158 <assert_contents>
999 <is_valid_xml/> 1159 <is_valid_xml/>
1000 </assert_contents> 1160 </assert_contents>
1001 </output> 1161 </output>
1162 <assert_stdout>
1163 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1164 </assert_stdout>
1002 </test> 1165 </test>
1003 <!-- TOPP_FileConverter_32 --> 1166 <!-- TOPP_FileConverter_32 -->
1004 <test expect_num_outputs="2"> 1167 <test expect_num_outputs="2">
1005 <section name="adv_opts"> 1168 <section name="adv_opts">
1006 <param name="UID_postprocessing" value="ensure"/> 1169 <param name="UID_postprocessing" value="ensure"/>
1013 <param name="write_scan_index" value="true"/> 1176 <param name="write_scan_index" value="true"/>
1014 <param name="lossy_compression" value="false"/> 1177 <param name="lossy_compression" value="false"/>
1015 <param name="lossy_mass_accuracy" value="-1.0"/> 1178 <param name="lossy_mass_accuracy" value="-1.0"/>
1016 <param name="process_lowmemory" value="false"/> 1179 <param name="process_lowmemory" value="false"/>
1017 <param name="no_peak_picking" value="false"/> 1180 <param name="no_peak_picking" value="false"/>
1181 <param name="no_zlib_compression" value="false"/>
1182 <param name="include_noise" value="false"/>
1018 <param name="force" value="false"/> 1183 <param name="force" value="false"/>
1019 <param name="test" value="true"/> 1184 <param name="test" value="true"/>
1020 </section> 1185 </section>
1021 <param name="in" value="FileConverter_32_input.mzML"/> 1186 <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"/> 1187 <output name="out" value="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1023 <param name="out_type" value="mzML"/> 1188 <param name="out_type" value="mzML"/>
1024 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1189 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1025 <output name="ctd_out" ftype="xml"> 1190 <output name="ctd_out" ftype="xml">
1026 <assert_contents> 1191 <assert_contents>
1027 <is_valid_xml/> 1192 <is_valid_xml/>
1028 </assert_contents> 1193 </assert_contents>
1029 </output> 1194 </output>
1195 <assert_stdout>
1196 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1197 </assert_stdout>
1030 </test> 1198 </test>
1031 <!-- TOPP_IDFileConverter_32_File_Conversion --> 1199 <!-- TOPP_IDFileConverter_32_File_Conversion -->
1032 <test expect_num_outputs="2"> 1200 <test expect_num_outputs="2">
1033 <section name="adv_opts"> 1201 <section name="adv_opts">
1034 <param name="UID_postprocessing" value="ensure"/> 1202 <param name="UID_postprocessing" value="ensure"/>
1041 <param name="write_scan_index" value="true"/> 1209 <param name="write_scan_index" value="true"/>
1042 <param name="lossy_compression" value="false"/> 1210 <param name="lossy_compression" value="false"/>
1043 <param name="lossy_mass_accuracy" value="-1.0"/> 1211 <param name="lossy_mass_accuracy" value="-1.0"/>
1044 <param name="process_lowmemory" value="false"/> 1212 <param name="process_lowmemory" value="false"/>
1045 <param name="no_peak_picking" value="false"/> 1213 <param name="no_peak_picking" value="false"/>
1214 <param name="no_zlib_compression" value="false"/>
1215 <param name="include_noise" value="false"/>
1046 <param name="force" value="false"/> 1216 <param name="force" value="false"/>
1047 <param name="test" value="true"/> 1217 <param name="test" value="true"/>
1048 </section> 1218 </section>
1049 <param name="in" value="IDFileConverter_32_output.tmp"/> 1219 <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"/> 1220 <output name="out" value="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
1051 <param name="out_type" value="mgf"/> 1221 <param name="out_type" value="mgf"/>
1052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1222 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1053 <output name="ctd_out" ftype="xml"> 1223 <output name="ctd_out" ftype="xml">
1054 <assert_contents> 1224 <assert_contents>
1055 <is_valid_xml/> 1225 <is_valid_xml/>
1056 </assert_contents> 1226 </assert_contents>
1057 </output> 1227 </output>
1228 <assert_stdout>
1229 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1230 </assert_stdout>
1058 </test> 1231 </test>
1059 <!-- TOPP_IDFileConverter_33_File_Conversion --> 1232 <!-- TOPP_IDFileConverter_33_File_Conversion -->
1060 <test expect_num_outputs="2"> 1233 <test expect_num_outputs="2">
1061 <section name="adv_opts"> 1234 <section name="adv_opts">
1062 <param name="UID_postprocessing" value="ensure"/> 1235 <param name="UID_postprocessing" value="ensure"/>
1069 <param name="write_scan_index" value="true"/> 1242 <param name="write_scan_index" value="true"/>
1070 <param name="lossy_compression" value="false"/> 1243 <param name="lossy_compression" value="false"/>
1071 <param name="lossy_mass_accuracy" value="-1.0"/> 1244 <param name="lossy_mass_accuracy" value="-1.0"/>
1072 <param name="process_lowmemory" value="false"/> 1245 <param name="process_lowmemory" value="false"/>
1073 <param name="no_peak_picking" value="false"/> 1246 <param name="no_peak_picking" value="false"/>
1247 <param name="no_zlib_compression" value="false"/>
1248 <param name="include_noise" value="false"/>
1074 <param name="force" value="false"/> 1249 <param name="force" value="false"/>
1075 <param name="test" value="true"/> 1250 <param name="test" value="true"/>
1076 </section> 1251 </section>
1077 <param name="in" value="IDFileConverter_33_output.tmp"/> 1252 <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"/> 1253 <output name="out" value="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
1079 <param name="out_type" value="mgf"/> 1254 <param name="out_type" value="mgf"/>
1080 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1081 <output name="ctd_out" ftype="xml"> 1256 <output name="ctd_out" ftype="xml">
1082 <assert_contents> 1257 <assert_contents>
1083 <is_valid_xml/> 1258 <is_valid_xml/>
1084 </assert_contents> 1259 </assert_contents>
1085 </output> 1260 </output>
1261 <assert_stdout>
1262 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1263 </assert_stdout>
1264 </test>
1265 <!-- TOPP_CometAdapter_2_prepare -->
1266 <test expect_num_outputs="2">
1267 <section name="adv_opts">
1268 <param name="UID_postprocessing" value="ensure"/>
1269 <param name="TIC_DTA2D" value="false"/>
1270 <param name="MGF_compact" value="false"/>
1271 <param name="force_MaxQuant_compatibility" value="false"/>
1272 <param name="force_TPP_compatibility" value="true"/>
1273 <param name="convert_to_chromatograms" value="false"/>
1274 <param name="change_im_format" value="none"/>
1275 <param name="write_scan_index" value="true"/>
1276 <param name="lossy_compression" value="false"/>
1277 <param name="lossy_mass_accuracy" value="-1.0"/>
1278 <param name="process_lowmemory" value="false"/>
1279 <param name="no_peak_picking" value="false"/>
1280 <param name="no_zlib_compression" value="false"/>
1281 <param name="include_noise" value="false"/>
1282 <param name="force" value="false"/>
1283 <param name="test" value="true"/>
1284 </section>
1285 <param name="in" value="CometAdapter_2_in.mzML"/>
1286 <output name="out" value="CometAdapter_2_prepared.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1287 <param name="out_type" value="mzML"/>
1288 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1289 <output name="ctd_out" ftype="xml">
1290 <assert_contents>
1291 <is_valid_xml/>
1292 </assert_contents>
1293 </output>
1294 <assert_stdout>
1295 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1296 </assert_stdout>
1086 </test> 1297 </test>
1087 <!-- TOPP_THERMORAWFILEPARSER_1 --> 1298 <!-- TOPP_THERMORAWFILEPARSER_1 -->
1088 <test expect_num_outputs="2"> 1299 <test expect_num_outputs="2">
1089 <section name="adv_opts"> 1300 <section name="adv_opts">
1090 <param name="UID_postprocessing" value="ensure"/> 1301 <param name="UID_postprocessing" value="ensure"/>
1097 <param name="write_scan_index" value="true"/> 1308 <param name="write_scan_index" value="true"/>
1098 <param name="lossy_compression" value="false"/> 1309 <param name="lossy_compression" value="false"/>
1099 <param name="lossy_mass_accuracy" value="-1.0"/> 1310 <param name="lossy_mass_accuracy" value="-1.0"/>
1100 <param name="process_lowmemory" value="false"/> 1311 <param name="process_lowmemory" value="false"/>
1101 <param name="no_peak_picking" value="false"/> 1312 <param name="no_peak_picking" value="false"/>
1313 <param name="no_zlib_compression" value="false"/>
1314 <param name="include_noise" value="false"/>
1102 <param name="force" value="false"/> 1315 <param name="force" value="false"/>
1103 <param name="test" value="true"/> 1316 <param name="test" value="true"/>
1104 </section> 1317 </section>
1105 <param name="in" value="ginkgotoxin-ms-switching.raw"/> 1318 <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"/> 1319 <output name="out" value="ginkgotoxin-ms-switching_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1107 <param name="out_type" value="mzML"/> 1320 <param name="out_type" value="mzML"/>
1108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1109 <output name="ctd_out" ftype="xml"> 1322 <output name="ctd_out" ftype="xml">
1110 <assert_contents> 1323 <assert_contents>
1111 <is_valid_xml/> 1324 <is_valid_xml/>
1112 </assert_contents> 1325 </assert_contents>
1113 </output> 1326 </output>
1114 </test> 1327 <assert_stdout>
1115 <test expect_num_outputs="1"> 1328 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1116 <param name="in" value="FileConverter_1_input.mzData"/> 1329 </assert_stdout>
1117 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 1330 </test>
1118 <param name="out_type" value="mzML"/> 1331 <!-- TOPP_SpectrastSearchAdapter_0_prepare -->
1119 </test> 1332 <test expect_num_outputs="2">
1120 </tests> 1333 <section name="adv_opts">
1334 <param name="UID_postprocessing" value="ensure"/>
1335 <param name="TIC_DTA2D" value="false"/>
1336 <param name="MGF_compact" value="false"/>
1337 <param name="force_MaxQuant_compatibility" value="false"/>
1338 <param name="force_TPP_compatibility" value="true"/>
1339 <param name="convert_to_chromatograms" value="false"/>
1340 <param name="change_im_format" value="none"/>
1341 <param name="write_scan_index" value="true"/>
1342 <param name="lossy_compression" value="false"/>
1343 <param name="lossy_mass_accuracy" value="-1.0"/>
1344 <param name="process_lowmemory" value="false"/>
1345 <param name="no_peak_picking" value="false"/>
1346 <param name="no_zlib_compression" value="false"/>
1347 <param name="include_noise" value="false"/>
1348 <param name="force" value="false"/>
1349 <param name="test" value="true"/>
1350 </section>
1351 <param name="in" value="spectra_spectrast.mzXML"/>
1352 <output name="out" value="SpectrastAdapter_1_hack.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
1353 <param name="out_type" value="mzML"/>
1354 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1355 <output name="ctd_out" ftype="xml">
1356 <assert_contents>
1357 <is_valid_xml/>
1358 </assert_contents>
1359 </output>
1360 <assert_stdout>
1361 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1362 </assert_stdout>
1363 </test>
1364 <test expect_num_outputs="1">
1365 <param name="in" value="FileConverter_1_input.mzData"/>
1366 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1367 <param name="out_type" value="mzML"/>
1368 </test>
1369 </tests>
1121 <help><![CDATA[Converts between different MS file formats. 1370 <help><![CDATA[Converts between different MS file formats.
1122 1371
1123 1372
1124 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileConverter.html]]></help> 1373 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileConverter.html]]></help>
1125 <expand macro="references"/> 1374 <expand macro="references"/>
1126 </tool> 1375 </tool>