Mercurial > repos > galaxyp > openms_targetedfileconverter
diff TargetedFileConverter.xml @ 12:43b9ed22e8ce 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 21:37:15 +0000 |
| parents | 9c70a651a53e |
| children |
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--- a/TargetedFileConverter.xml Thu Dec 01 19:21:24 2022 +0000 +++ b/TargetedFileConverter.xml Fri Jun 14 21:37:15 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: [Targeted Experiments]--> +<!--Proposed Tool Section: [File Converter]--> <tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description> + <description>Converts different transition files for targeted proteomics / metabolomics analysis</description> <macros> <token name="@EXECUTABLE@">TargetedFileConverter</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 @@ -39,15 +38,16 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> - <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense"> + <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/TOPP_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> + <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense"> <option value="TraML">traml</option> <option value="pqp">pqp</option> <option value="tsv">tabular (tsv)</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> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> - <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="true" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help=""> + <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help=""> <option value="iRT" selected="true">iRT</option> <option value="seconds">seconds</option> <option value="minutes">minutes</option> @@ -59,7 +59,7 @@ <expand macro="adv_opts_macro"> <param argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" 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> @@ -78,7 +78,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_ConvertTSVToTraML_test_1 --> + <tests> + <!-- TOPP_ConvertTSVToTraML_test_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="false"/> @@ -86,7 +87,7 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -99,6 +100,9 @@ <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_ConvertTSVToTraML_test_2 --> <test expect_num_outputs="2"> @@ -108,7 +112,7 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="minutes"/> @@ -121,6 +125,9 @@ <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_ConvertTSVToTraML_test_3 --> <test expect_num_outputs="2"> @@ -130,7 +137,7 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="seconds"/> @@ -143,6 +150,9 @@ <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_ConvertTSVToTraML_test_4 --> <test expect_num_outputs="2"> @@ -152,7 +162,57 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> - <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_ConvertTSVToTraML_test_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> + <output name="out" value="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_ConvertTSVToTraML_test_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> + <output name="out" value="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -165,16 +225,19 @@ <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_ConvertTSVToTraML_test_5 --> + <!-- TOPP_ConvertTSVToTraML_test_7 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> + <output name="out" value="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -187,16 +250,44 @@ <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_ConvertTSVToTraML_test_6 --> + <!-- TOPP_TargetedFileConverter_test_1_prepare --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="TargetedFileConverter_1_input.TraML"/> + <output name="out" value="TargetedFileConverter_1_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" value="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -209,16 +300,19 @@ <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_ConvertTSVToTraML_test_7 --> + <!-- TOPP_TargetedFileConverter_test_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> - <param name="legacy_traml_id" value="false"/> + <param name="legacy_traml_id" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" value="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -231,16 +325,44 @@ <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_TargetedFileConverter_test_1 --> + <!-- TOPP_TargetedFileConverter_test_3_prepare --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="TargetedFileConverter_3_input.TraML"/> + <output name="out" value="TargetedFileConverter_3_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" value="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -253,16 +375,19 @@ <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_TargetedFileConverter_test_2 --> + <!-- TOPP_TargetedFileConverter_test_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" value="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -275,16 +400,19 @@ <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_TargetedFileConverter_test_3 --> + <!-- TOPP_TargetedFileConverter_test_10_prepare --> <test expect_num_outputs="2"> <section name="adv_opts"> - <param name="legacy_traml_id" value="false"/> + <param name="legacy_traml_id" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="in" value="TargetedFileConverter_10_input.pqp"/> + <output name="out" value="TargetedFileConverter_10_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -297,28 +425,9 @@ <is_valid_xml/> </assert_contents> </output> - </test> - <!-- TOPP_TargetedFileConverter_test_4 --> - <test expect_num_outputs="2"> - <section name="adv_opts"> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </section> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <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_TargetedFileConverter_test_10 --> <test expect_num_outputs="2"> @@ -328,7 +437,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -341,6 +450,34 @@ <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_TargetedFileConverter_test_11_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_11_input.TraML"/> + <output name="out" value="TargetedFileConverter_11_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_11 --> <test expect_num_outputs="2"> @@ -350,7 +487,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -363,6 +500,34 @@ <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_TargetedFileConverter_test_8_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_8_input.tsv" ftype="tabular"/> + <output name="out" value="TargetedFileConverter_8_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_8 --> <test expect_num_outputs="2"> @@ -372,7 +537,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -385,6 +550,34 @@ <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_TargetedFileConverter_test_9_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_9_input.TraML"/> + <output name="out" value="TargetedFileConverter_9_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_9 --> <test expect_num_outputs="2"> @@ -394,7 +587,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -407,6 +600,9 @@ <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_TargetedFileConverter_test_5 --> <test expect_num_outputs="2"> @@ -416,7 +612,7 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="ConvertTraMLToTSV_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -429,6 +625,34 @@ <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_TargetedFileConverter_test_12_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_12_input.TraML"/> + <output name="out" value="TargetedFileConverter_12_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_TargetedFileConverter_test_12 --> <test expect_num_outputs="2"> @@ -438,7 +662,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -451,6 +675,9 @@ <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_TargetedFileConverter_test_13 --> <test expect_num_outputs="2"> @@ -460,7 +687,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> - <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -473,6 +700,9 @@ <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_TargetedFileConverter_test_6 --> <test expect_num_outputs="2"> @@ -482,7 +712,7 @@ <param name="test" value="true"/> </section> <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="ConvertTraMLToTSV_output_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -495,8 +725,86 @@ <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> - <!-- UTILS_AssayGeneratorMetabo_6 --> + <!-- TOPP_OpenSwathWorkflow_13_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathWorkflow_1_input.TraML"/> + <output name="out" value="OpenSwathWorkflow_13_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_OpenSwathWorkflow_14_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathWorkflow_1_input.TraML"/> + <output name="out" value="OpenSwathWorkflow_14_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_OpenSwathWorkflow_17_b_prepare --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> + <output name="out" value="OpenSwathWorkflow_17_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/> + <param name="out_type" value="pqp"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <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_AssayGeneratorMetabo_6 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="legacy_traml_id" value="false"/> @@ -504,7 +812,7 @@ <param name="test" value="true"/> </section> <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus_traml.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <section name="algorithm"> <param name="retentionTimeInterpretation" value="iRT"/> @@ -517,11 +825,14 @@ <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> </tests> <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TargetedFileConverter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TargetedFileConverter.html]]></help> <expand macro="references"/> </tool>