Mercurial > repos > galaxyp > openms_fileconverter
diff FileConverter.xml @ 16:8b6336c903ef draft default tip
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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--- a/FileConverter.xml Thu Dec 01 19:09:16 2022 +0000 +++ b/FileConverter.xml Fri Jun 14 21:33:58 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [File Handling]--> +<!--Proposed Tool Section: [File Converter]--> <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Converts between different MS file formats.</description> + <description>Converts between different MS file formats</description> <macros> <token name="@EXECUTABLE@">FileConverter</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,8 +38,8 @@ <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <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)"/> - <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"> + <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)"/> + <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"> <option value="consensusXML">consensusxml</option> <option value="csv">csv</option> <option value="dta2d">dta2d</option> @@ -51,10 +50,11 @@ <option value="mzML">mzml</option> <option value="mzXML">mzxml</option> <option value="oms">sqlite (oms)</option> + <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> <expand macro="list_string_san" name="out_type"/> </param> <expand macro="adv_opts_macro"> - <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"> + <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"> <option value="none">none</option> <option value="ensure" selected="true">ensure</option> <option value="reassign">reassign</option> @@ -65,7 +65,7 @@ <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=""/> <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=""/> <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=""/> - <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=""> + <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=""> <option value="none" selected="true">none</option> <option value="concatenated">concatenated</option> <option value="multiple_spectra">multiple_spectra</option> @@ -74,11 +74,13 @@ </param> <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"/> <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=""/> - <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)"/> + <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)"/> <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"/> <param argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/> + <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"/> + <param argument="-include_noise" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include noise data in mzML output" help=""/> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -104,7 +106,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_FileConverter_1 --> + <tests> + <!-- TOPP_FileConverter_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="UID_postprocessing" value="ensure"/> @@ -119,11 +122,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -131,6 +136,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_2 --> <test expect_num_outputs="2"> @@ -147,11 +155,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_2_input.someInputDTA2D"/> - <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -159,6 +169,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_3 --> <test expect_num_outputs="2"> @@ -175,11 +188,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_3_input.featureXML"/> - <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -187,6 +202,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_4 --> <test expect_num_outputs="2"> @@ -203,11 +221,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -215,6 +235,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_5 --> <test expect_num_outputs="2"> @@ -231,11 +254,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_5_input.mzML"/> - <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> + <output name="out" value="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> <param name="out_type" value="mzXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -243,6 +268,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_6 --> <test expect_num_outputs="2"> @@ -259,11 +287,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_6_input.mzML"/> - <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> + <output name="out" value="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> <param name="out_type" value="mzXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -271,6 +301,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_7 --> <test expect_num_outputs="2"> @@ -287,11 +320,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_7_input.consensusXML"/> - <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -299,6 +334,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_8 --> <test expect_num_outputs="2"> @@ -315,11 +353,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_8_input.mzML"/> - <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/> + <output name="out" value="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/> <param name="out_type" value="mzData"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -327,6 +367,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_9 --> <test expect_num_outputs="2"> @@ -343,11 +386,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_9_input.consensusXML"/> - <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -355,6 +400,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_10 --> <test expect_num_outputs="2"> @@ -371,11 +419,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -383,6 +433,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_11 --> <test expect_num_outputs="2"> @@ -399,11 +452,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_11_input.peplist"/> - <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -411,6 +466,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_12 --> <test expect_num_outputs="2"> @@ -427,11 +485,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> - <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -439,6 +499,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_13 --> <test expect_num_outputs="2"> @@ -455,11 +518,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_13_input.peptides.kroenik"/> - <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -467,6 +532,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_14 --> <test expect_num_outputs="2"> @@ -483,11 +551,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_9_output.featureXML"/> - <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <param name="out_type" value="consensusXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -495,6 +565,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_15 --> <test expect_num_outputs="2"> @@ -511,11 +584,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <param name="out_type" value="consensusXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -523,6 +598,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_16 --> <test expect_num_outputs="2"> @@ -539,11 +617,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <param name="out_type" value="consensusXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -551,6 +631,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_17 --> <test expect_num_outputs="2"> @@ -567,11 +650,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="out_type" value="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -579,6 +664,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_18 --> <test expect_num_outputs="2"> @@ -595,11 +683,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="out_type" value="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -607,6 +697,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_19 --> <test expect_num_outputs="2"> @@ -623,11 +716,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="true"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -635,6 +730,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_20 --> <test expect_num_outputs="2"> @@ -651,11 +749,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_20_input.featureXML"/> - <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="out_type" value="featureXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -663,6 +763,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_21 --> <test expect_num_outputs="2"> @@ -679,11 +782,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="true"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -691,6 +796,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_23 --> <test expect_num_outputs="2"> @@ -707,11 +815,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_23_input.mzML"/> - <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -719,6 +829,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_24 --> <test expect_num_outputs="2"> @@ -735,11 +848,13 @@ <param name="lossy_mass_accuracy" value="0.0001"/> <param name="process_lowmemory" value="true"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -747,6 +862,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_25 --> <test expect_num_outputs="2"> @@ -763,11 +881,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="true"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -775,6 +895,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_26 --> <test expect_num_outputs="2"> @@ -791,11 +914,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> + <output name="out" value="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> <param name="out_type" value="mzXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -803,6 +928,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_26-2 --> <test expect_num_outputs="2"> @@ -819,11 +947,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_26_output.mzXML"/> - <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> + <output name="out" value="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/> <param name="out_type" value="mzXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -831,6 +961,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_27 --> <test expect_num_outputs="2"> @@ -847,11 +980,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_27_input.mzML"/> - <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -859,6 +994,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_28 --> <test expect_num_outputs="2"> @@ -875,11 +1013,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_28_input.mzML"/> - <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -887,6 +1027,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_29 --> <test expect_num_outputs="2"> @@ -903,11 +1046,13 @@ <param name="lossy_mass_accuracy" value="1e-05"/> <param name="process_lowmemory" value="true"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -915,6 +1060,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_29_back --> <test expect_num_outputs="2"> @@ -931,11 +1079,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_29_output.mzML"/> - <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/> + <output name="out" value="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -943,6 +1093,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_30 --> <test expect_num_outputs="2"> @@ -959,11 +1112,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_30_input.mzML"/> - <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -971,6 +1126,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_31 --> <test expect_num_outputs="2"> @@ -987,11 +1145,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_30_output.mzML"/> - <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -999,6 +1159,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_FileConverter_32 --> <test expect_num_outputs="2"> @@ -1015,11 +1178,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileConverter_32_input.mzML"/> - <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -1027,6 +1192,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_IDFileConverter_32_File_Conversion --> <test expect_num_outputs="2"> @@ -1043,11 +1211,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="IDFileConverter_32_output.tmp"/> - <output name="out" file="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> + <output name="out" value="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> <param name="out_type" value="mgf"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -1055,6 +1225,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_IDFileConverter_33_File_Conversion --> <test expect_num_outputs="2"> @@ -1071,11 +1244,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="IDFileConverter_33_output.tmp"/> - <output name="out" file="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> + <output name="out" value="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> <param name="out_type" value="mgf"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -1083,6 +1258,42 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> + </test> + <!-- TOPP_CometAdapter_2_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="UID_postprocessing" value="ensure"/> + <param name="TIC_DTA2D" value="false"/> + <param name="MGF_compact" value="false"/> + <param name="force_MaxQuant_compatibility" value="false"/> + <param name="force_TPP_compatibility" value="true"/> + <param name="convert_to_chromatograms" value="false"/> + <param name="change_im_format" value="none"/> + <param name="write_scan_index" value="true"/> + <param name="lossy_compression" value="false"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="CometAdapter_2_in.mzML"/> + <output name="out" value="CometAdapter_2_prepared.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_THERMORAWFILEPARSER_1 --> <test expect_num_outputs="2"> @@ -1099,11 +1310,13 @@ <param name="lossy_mass_accuracy" value="-1.0"/> <param name="process_lowmemory" value="false"/> <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ginkgotoxin-ms-switching.raw"/> - <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="ginkgotoxin-ms-switching_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="out_type" value="mzML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -1111,16 +1324,52 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> - <test expect_num_outputs="1"> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> -</test> -</tests> + <!-- TOPP_SpectrastSearchAdapter_0_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="UID_postprocessing" value="ensure"/> + <param name="TIC_DTA2D" value="false"/> + <param name="MGF_compact" value="false"/> + <param name="force_MaxQuant_compatibility" value="false"/> + <param name="force_TPP_compatibility" value="true"/> + <param name="convert_to_chromatograms" value="false"/> + <param name="change_im_format" value="none"/> + <param name="write_scan_index" value="true"/> + <param name="lossy_compression" value="false"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="no_peak_picking" value="false"/> + <param name="no_zlib_compression" value="false"/> + <param name="include_noise" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra_spectrast.mzXML"/> + <output name="out" value="SpectrastAdapter_1_hack.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> + </test> + <test expect_num_outputs="1"> + <param name="in" value="FileConverter_1_input.mzData"/> + <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + </test> + </tests> <help><![CDATA[Converts between different MS file formats. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileConverter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileConverter.html]]></help> <expand macro="references"/> </tool>