Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher
diff OpenSwathMzMLFileCacher.xml @ 13:f82b320ceb90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:04:12 +0000 |
parents | fc775d5aa321 |
children | fe39f583c19a |
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--- a/OpenSwathMzMLFileCacher.xml Fri Nov 06 19:51:52 2020 +0000 +++ b/OpenSwathMzMLFileCacher.xml Thu Dec 01 19:04:12 2022 +0000 @@ -1,13 +1,11 @@ <?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]--> -<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> <macros> <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,21 +39,21 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> - <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense"> + <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass 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: that not all conversion paths work or make sense"> <option value="mzML">mzml</option> <option value="sqMass">sqmass</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="out_type"/> </param> - <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/> - <param name="full_meta" argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/> + <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/> + <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/> <expand macro="adv_opts_macro"> - <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> - <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/> - <param name="lowmem_batchsize" argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <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="-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="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" 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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -63,9 +61,8 @@ </param> </inputs> <outputs> - <data name="out" label="${tool.name} on ${on_string}: out"> + <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"> <change_format> - <when input="out_type" value="mzML" format="mzml"/> <when input="out_type" value="sqMass" format="sqmass"/> </change_format> </data> @@ -73,13 +70,220 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_OpenSwathMzMLFileCacher"/> - <expand macro="manutest_OpenSwathMzMLFileCacher"/> + <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> + <param name="out_type" value="sqMass"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> + <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> + <param name="out_type" value="sqMass"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> + <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="true"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathWorkflow_14_step2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> + <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="false"/> + <param name="full_meta" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> <expand macro="references"/> </tool>