Mercurial > repos > galaxyp > openms_msfraggeradapter
changeset 6:907fda39b333 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 21:28:16 +0000 |
| parents | 9866e1170611 |
| children | |
| files | MSFraggerAdapter.xml fill_ctd_clargs.py generate-foo.sh get_tests.py macros.xml prepare_test_data_manual.sh readme.md test-data.sh |
| diffstat | 8 files changed, 548 insertions(+), 515 deletions(-) [+] |
line wrap: on
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--- a/MSFraggerAdapter.xml Thu Dec 01 19:05:24 2022 +0000 +++ b/MSFraggerAdapter.xml Fri Jun 14 21:28:16 2024 +0000 @@ -1,22 +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: [Utilities]--> +<!--Proposed Tool Section: []--> <tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Peptide Identification with MSFragger. -Important note: -The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute -the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available -for use on related service offerings supported by the University of Tubingen and the Center for -Integrative Bioinformatics. -Per the license agreement the use of the pipeline and associated materials is for academic -research, non-commercial or educational purposes. Any commercial use inquiries -must be directed to the University of Michigan Technology Transfer Office at -techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the -University of Michigan. - -For details, please see the supplied license file or -https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt -</description> + <description>Peptide Identification with MSFragger</description> <macros> <token name="@EXECUTABLE@">MSFraggerAdapter</token> <import>macros.xml</import> @@ -29,13 +14,13 @@ ## 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($in.ext)' && mkdir out && #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir opt_out && #end if mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && ## Main program call @@ -70,36 +55,37 @@ <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-license" display="radio" type="select" optional="false" label="Set to yes, if you have read and agreed to the MSFragger license terms" help=""> + <param argument="-license" type="select" label="Set to yes, if you have read and agreed to the MSFragger license terms" help=""> <option value="yes">yes</option> <option value="no">no</option> + <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> <expand macro="list_string_san" name="license"/> </param> - <param argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/> - <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/> - <param argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/> + <param argument="-java_heapmemory" type="integer" value="3500" label="Maximum Java heap size (in MB)" help=""/> + <param argument="-in" type="data" format="mzml,mzxml" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/> + <param argument="-database" type="data" format="fasta" label="Protein FASTA database file path" help=" select fasta data sets(s)"/> <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/> <section name="tolerance" title="Search Tolerances" help="" expanded="false"> - <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" optional="true" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/> - <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" optional="true" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/> - <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> + <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/> + <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/> + <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="precursor_mass_unit"/> </param> - <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="true" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/> - <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" optional="true" label="Unit of precursor true tolerance" help=""> + <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/> + <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" label="Unit of precursor true tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="precursor_true_unit"/> </param> - <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/> - <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> + <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/> + <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" label="Unit of fragment mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="fragment_mass_unit"/> </param> - <param name="isotope_error" argument="-tolerance:isotope_error" type="select" optional="true" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12"> + <param name="isotope_error" argument="-tolerance:isotope_error" type="select" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12"> <option value="0" selected="true">0</option> <option value="1">1</option> <option value="2">2</option> @@ -108,25 +94,23 @@ </param> </section> <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false"> - <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="true" label="Name of the enzyme to be written to the pepXML file" help=""> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" label="Name of the enzyme to be written to the pepXML file" help=""> <option value="no cleavage">no cleavage</option> <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Arg-C">Arg-C</option> <option value="Arg-C/P">Arg-C/P</option> <option value="Asp-N">Asp-N</option> - <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="Trypsin" selected="true">Trypsin</option> + <option value="Arg-C">Arg-C</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> <option value="Formic_acid">Formic_acid</option> @@ -137,26 +121,28 @@ <option value="TrypChymo">TrypChymo</option> <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="iodosobenzoate">iodosobenzoate</option> <option value="staphylococcal protease/D">staphylococcal protease/D</option> - <option value="Trypsin" selected="true">Trypsin</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <expand macro="list_string_san" name="search_enzyme_name"/> </param> - <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help=""> + <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help=""> <expand macro="list_string_san" name="search_enzyme_cutafter"/> </param> - <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="true" value="P" label="Residues that the enzyme will not cut before" help=""> + <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" value="P" label="Residues that the enzyme will not cut before" help=""> <expand macro="list_string_san" name="search_enzyme_nocutbefore"/> </param> - <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" optional="true" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help=""> + <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help=""> <option value="non-enzymatic">non-enzymatic</option> <option value="semi">semi</option> <option value="fully" selected="true">fully</option> <expand macro="list_string_san" name="num_enzyme_termini"/> </param> - <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="true" label="Allowed number of missed cleavages" help=""> + <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" label="Allowed number of missed cleavages" help=""> <option value="0">0</option> <option value="1">1</option> <option value="2" selected="true">2</option> @@ -165,10 +151,10 @@ <option value="5">5</option> <expand macro="list_string_san" name="allowed_missed_cleavage"/> </param> - <param name="min_length" argument="-digest:min_length" type="integer" optional="true" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/> - <param name="max_length" argument="-digest:max_length" type="integer" optional="true" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/> - <param name="mass_range_min" argument="-digest:mass_range_min" type="float" optional="true" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/> - <param name="mass_range_max" argument="-digest:mass_range_max" type="float" optional="true" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/> + <param name="min_length" argument="-digest:min_length" type="integer" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/> + <param name="max_length" argument="-digest:max_length" type="integer" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/> + <param name="mass_range_min" argument="-digest:mass_range_min" type="float" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/> + <param name="mass_range_max" argument="-digest:mass_range_max" type="float" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/> </section> <section name="varmod" title="Variable Modification Parameters" help="" expanded="false"> <param name="clip_nterm_m" argument="-varmod:clip_nterm_m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Specifies the trimming of a protein N-terminal methionine as a variable modification" help=""/> @@ -185,7 +171,7 @@ </param> <param name="enable_common" argument="-varmod:enable_common" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable common variable modifications (15.9949 M and 42.0106 [^)" help=""/> <param name="not_allow_multiple_variable_mods_on_residue" argument="-varmod:not_allow_multiple_variable_mods_on_residue" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not allow any one amino acid to be modified by multiple variable modifications" help=""/> - <param name="max_variable_mods_per_peptide" argument="-varmod:max_variable_mods_per_peptide" type="select" optional="true" label="Maximum total number of variable modifications per peptide" help=""> + <param name="max_variable_mods_per_peptide" argument="-varmod:max_variable_mods_per_peptide" type="select" label="Maximum total number of variable modifications per peptide" help=""> <option value="0">0</option> <option value="1">1</option> <option value="2" selected="true">2</option> @@ -194,15 +180,15 @@ <option value="5">5</option> <expand macro="list_string_san" name="max_variable_mods_per_peptide"/> </param> - <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" optional="true" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/> + <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/> </section> <section name="spectrum" title="Spectrum Processing Parameters" help="" expanded="false"> - <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" optional="true" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/> - <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" optional="true" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/> - <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/> - <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> - <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> - <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" optional="true" label="Maximum charge state for theoretical fragments to match" help=""> + <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/> + <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/> + <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/> + <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> + <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> + <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" label="Maximum charge state for theoretical fragments to match" help=""> <option value="1">1</option> <option value="2" selected="true">2</option> <option value="3">3</option> @@ -210,45 +196,45 @@ <expand macro="list_string_san" name="max_fragment_charge"/> </param> <param name="override_charge" argument="-spectrum:override_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)" help=""/> - <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" optional="true" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/> - <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" optional="true" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/> + <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/> + <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/> </section> <section name="search" title="Open Search Features" help="" expanded="false"> - <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" optional="true" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/> - <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" optional="true" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/> - <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" optional="true" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/> - <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" optional="true" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/> - <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" optional="true" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/> - <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" optional="true" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/> - <param name="output_report_topn" argument="-search:output_report_topn" type="integer" optional="true" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/> - <param name="output_max_expect" argument="-search:output_max_expect" type="float" optional="true" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/> - <param name="localize_delta_mass" argument="-search:localize_delta_mass" type="integer" optional="true" min="0" value="0" label="Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)" help=""/> + <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/> + <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/> + <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/> + <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/> + <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/> + <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/> + <param name="output_report_topn" argument="-search:output_report_topn" type="integer" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/> + <param name="output_max_expect" argument="-search:output_max_expect" type="float" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/> + <param name="localize_delta_mass" argument="-search:localize_delta_mass" type="integer" min="0" value="0" label="Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)" help=""/> </section> <section name="statmod" title="Static Modification Parameters" help="" expanded="false"> - <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/> - <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/> - <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/> - <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/> - <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/> - <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/> - <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to serine" help=""/> - <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to proline" help=""/> - <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to valine" help=""/> - <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/> - <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" optional="true" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/> - <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/> - <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/> - <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/> - <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/> - <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/> - <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/> - <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/> - <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/> - <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/> - <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/> - <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/> - <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/> - <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/> + <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/> + <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/> + <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/> + <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/> + <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/> + <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/> + <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" min="0.0" value="0.0" label="Statically add mass to serine" help=""/> + <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" min="0.0" value="0.0" label="Statically add mass to proline" help=""/> + <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" min="0.0" value="0.0" label="Statically add mass to valine" help=""/> + <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/> + <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/> + <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/> + <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/> + <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/> + <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/> + <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/> + <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/> + <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/> + <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/> + <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/> + <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/> + <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/> + <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/> + <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/> <param name="unimod" argument="-statmod:unimod" type="text" optional="true" value="" label="Fixed modifications in unimod syntax if specific mass is unknown" help="e.g. Carbamidomethylation (C). When multiple different masses are given for one aminoacid this parameter (unimod) will have priority (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="unimod"/> <expand macro="list_string_san" name="unimod"/> @@ -258,12 +244,12 @@ <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> <expand macro="list_string_san" name="decoy_string"/> </param> - <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> + <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> <option value="prefix" selected="true">prefix</option> <option value="suffix">suffix</option> <expand macro="list_string_san" name="decoy_string_position"/> </param> - <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> + <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> <option value="error">error</option> <option value="warn" selected="true">warn</option> <option value="silent">silent</option> @@ -272,54 +258,55 @@ <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> - <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> + <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> <option value="error" selected="true">error</option> <option value="warn">warn</option> <option value="remove">remove</option> <expand macro="list_string_san" name="unmatched_action"/> </param> - <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> - <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> + <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> + <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> + <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/> <section name="enzyme" title="" help="" expanded="false"> - <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> + <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> <option value="auto" selected="true">auto</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="Arg-C">Arg-C</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Asp-N">Asp-N</option> <option value="Asp-N/B">Asp-N/B</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> <option value="Formic_acid">Formic_acid</option> - <option value="Trypsin">Trypsin</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-N">Lys-N</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <option value="staphylococcal protease/D">staphylococcal protease/D</option> - <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> <option value="no cleavage">no cleavage</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Asp-N">Asp-N</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> <option value="Lys-C/P">Lys-C/P</option> <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="Arg-C">Arg-C</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Trypsin">Trypsin</option> <expand macro="list_string_san" name="name"/> </param> - <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> + <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> <option value="auto" selected="true">auto</option> <option value="full">full</option> <option value="semi">semi</option> @@ -330,7 +317,7 @@ </section> <expand macro="adv_opts_macro"> <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> @@ -348,12 +335,13 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_MSFraggerAdapter_7 --> + <tests> + <!-- TOPP_MSFraggerAdapter_7 --> <!-- TOPP_MSFraggerAdapter_8 --> </tests> <help><![CDATA[Peptide Identification with MSFragger. Important note: -The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute +The Regents of the University of Michigan ("Michigan") grants us permission to redistribute the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available for use on related service offerings supported by the University of Tubingen and the Center for Integrative Bioinformatics. @@ -368,6 +356,6 @@ -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSFraggerAdapter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSFraggerAdapter.html]]></help> <expand macro="references"/> </tool>
--- a/fill_ctd_clargs.py Thu Dec 01 19:05:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ -#!/usr/bin/env python3 - -import operator -from argparse import ArgumentParser -from functools import reduce # forward compatibility for Python 3 -from io import StringIO - -from CTDopts.CTDopts import ( - _Null, - CTDModel, - ModelTypeError, - Parameters -) - - -def getFromDict(dataDict, mapList): - return reduce(operator.getitem, mapList, dataDict) - - -def setInDict(dataDict, mapList, value): - getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value - - -if __name__ == "__main__": - # note add_help=False since otherwise arguments starting with -h will - # trigger an error (despite allow_abbreviate) - parser = ArgumentParser(prog="fill_ctd_clargs", - description="fill command line arguments" - "into a CTD file and write the CTD file to stdout", - add_help=False, allow_abbrev=False) - parser.add_argument("--ini_file", dest="ini_file", help="input ini file", - metavar='INI', default=None, required=True) - parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" - "if given then optional parameters from the ini file" - "will be filled with the defaults from this CTD file", - metavar='CTD', default=None, required=False) - args, cliargs = parser.parse_known_args() - - # load CTDModel - ini_model = None - try: - ini_model = CTDModel(from_file=args.ini_file) - except ModelTypeError: - pass - try: - ini_model = Parameters(from_file=args.ini_file) - except ModelTypeError: - pass - assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) - - # get a dictionary of the ctd arguments where the values of the parameters - # given on the command line are overwritten - ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) - - if args.ctd_file: - ctd_model = CTDModel(from_file=args.ctd_file) - ctd_values = ctd_model.get_defaults() - for param in ini_model.get_parameters(): - if not param.required and (param.default is None or type(param.default) is _Null): - lineage = param.get_lineage(name_only=True) - try: - default = getFromDict(ctd_values, lineage) - except KeyError: - continue - setInDict(ini_values, lineage, default) - - # write the ctd with the values taken from the dictionary - out = StringIO() - ctd_tree = ini_model.write_ctd(out, ini_values) - print(out.getvalue())
--- a/generate-foo.sh Thu Dec 01 19:05:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,215 +0,0 @@ -#!/usr/bin/env bash - -# parse test definitions from OpenMS sources for a tool with a given id -function get_tests2 { - id=$1 - >&2 echo "generate tests for $id" - echo '<xml name="autotest_'"$id"'">' - - # get the tests from the CMakeLists.txt - # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 - # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt - # - several tools with duplicated input (leads to conflict when linking) - # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) - # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) - # - some input files are originally in a subdir (degenerated cases/), but not in test-data - # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) - # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 - # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 - CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | - sed 's@${DATA_DIR_SHARE}/@@g' | - grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | - sed 's/${TMP_RIP_PATH}/""/' | - grep -v "MaRaClusterAdapter.*-consensus_out"| - grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | - sed 's@degenerate_cases/@@g' | - egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | - grep -v '"TOPP_SiriusAdapter_10"') - - # 1st part is a dirty hack to join lines containing a single function call, e.g. - # addtest(.... - # ....) - echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | - grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line - do - line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g') - # >&2 echo $line - test_id=$(echo "$line" | cut -d" " -f 1) - tool_id=$(echo "$line" | cut -d" " -f 2) - # >&2 echo "test_id $test_id" - if [[ $test_id =~ _out_?[0-9]? ]]; then - >&2 echo " skip $test_id $line" - continue - fi - if [[ ${id,,} != ${tool_id,,} ]]; then - >&2 echo " skip $test_id ($id != $tool_id) $line" - continue - fi - - #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) - if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then - >&2 echo " skip failing "$test_id - continue - fi - tes=" <test>\n" - line=$(fix_tmp_files "$line") - line=$(unique_files "$line") - # >&2 echo LINE $line - #if there is an ini file then we use this to generate the test - #otherwise the ctd file is used - #other command line parameters are inserted later into this xml - if grep -lq "\-ini" <<<"$line"; then - ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/') - ini="test-data/$ini" - else - ini="ctd/$tool_id.ctd" - fi - # >&2 echo "========================================================" - # >&2 echo "USING ini $ini" - cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') - - ctdtmp=$(mktemp) - # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) - # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" - eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" - # >&2 echo $ctdtmp - # >&2 cat $ctdtmp - testtmp=$(mktemp) - # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" - CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null - echo "<!-- $test_id -->" - cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - - rm "$ctdtmp" "$testtmp" - - #> /dev/null - - #rm $testtmp - done - echo '</xml>' -} - -#some tests use the same file twice which does not work in planemo tests -#hence we create symlinks for each file used twice -function unique_files { - line=$@ - for arg in $@ - do - if [[ ! -f "test-data/$arg" ]]; then - continue - fi - cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) - while [[ $cnt -gt 1 ]]; do - new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./") - ln -fs $arg test-data/$new_arg - line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/") - cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) - done - done - - echo $line -} - -# options of out_type selects need to be fixed to Galaxy data types -function fix_out_type { - grep "^$1" "$2" | awk '{print $2}' -} - -#OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. -#problem: the extension of the tmp files is unusable for test generation. -#unfortunately the extensions used in the DIFF lines are not always usable for the CLI -#(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) -#this function replaces the tmp file by the expected file. -function fix_tmp_files { - # >&2 echo "FIX $line" - ret="" - for a in $@; do - # >&2 echo " a "$a - if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then - ret="$ret $a" - continue - fi - diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") - # >&2 echo " diff_line "$diff_line - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) - # >&2 echo " in1 "$in1 - if [[ "$a" != "$in1" ]]; then - ret="$ret $a" - continue - fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) - in2=$(basename $in2 | sed 's/)$//') - # >&2 echo " in2 "$in2 - if [[ -f "test-data/$in2" ]]; then - ln -fs "$in1" "test-data/$in2" - ret="$ret $in2" - else - ret="$ret $a" - fi - done -# >&2 echo "--> $ret" - echo "$ret" -} - -function link_tmp_files { - # note this also considers commented lines (starting with a #) - # because of tests where the diff command is commented and we - # still want to use the extension of these files - cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line - do - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line) - in1=$(basename $in1 | sed 's/)$//') - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line) - in2=$(basename $in2 | sed 's/)$//') - if [[ "$in1" == "$in2" ]]; then - >&2 echo "not linking equal $in1 $in2" - continue - fi - ln -f -s $in1 test-data/$in2 - done - - find test-data/ -name "*.tmp" -print0 | - while IFS= read -r -d '' i; do - if [ ! -e test-data/$(basename $i .tmp) ]; then - ln -s $(basename $i) test-data/$(basename $i .tmp) - else - ln -fs $(basename $i) test-data/$(basename $i .tmp) - fi - done -} - - - -# parse data preparation calls from OpenMS sources for a tool with a given id -function prepare_test_data { -# id=$1 -# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" - - # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 - cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | - sed 's/degenerate_cases\///' | - egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | - grep add_test | - egrep "TOPP|UTILS" | - sed 's@${DATA_DIR_SHARE}/@@g;'| - sed 's@${TMP_RIP_PATH}@./@g'| - sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | - while read line - do - test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) - - if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then - >&2 echo " skip failing "$test_id - continue - fi - - line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) - # line="$(fix_tmp_files $line)" - echo 'echo executing "'$test_id'"' - echo "$line > $test_id.stdout 2> $test_id.stderr" - echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" - done -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_tests.py Fri Jun 14 21:28:16 2024 +0000 @@ -0,0 +1,344 @@ +#!/usr/bin/env python + +import argparse +import os.path +import re +import shlex +import sys +import tempfile +from typing import ( + Dict, + List, + Optional, + TextIO, + Tuple, +) + +from ctdconverter.common.utils import ( + ParameterHardcoder, + parse_hardcoded_parameters, + parse_input_ctds, +) +from ctdconverter.galaxy.converter import convert_models +from CTDopts.CTDopts import ( + CTDModel, + ModelTypeError, + Parameters, +) + +SKIP_LIST = [ + r"_prepare\"", + r"_convert", + r"WRITEINI", + r"WRITECTD", + r"INVALIDVALUE", + r"\.ini\.json", + r"OpenSwathMzMLFileCacher .*-convert_back", # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 + r"MaRaClusterAdapter.*-consensus_out", # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) + r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ", # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) + r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$', # no suppert for cached mzML + r'TOPP_SiriusAdapter_[0-9]+$', # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway + r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$' # Skip AssayGeneratorMetabo tests using Sirius https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools) +] + + +def get_failing_tests(cmake: List[str]) -> List[str]: + failing_tests = [] + re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)") + + for cmake in args.cmake: + with open(cmake) as cmake_fh: + for line in cmake_fh: + match = re_fail.search(line) + if match: + failing_tests.append(match.group(1)) + return failing_tests + + +def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str: + """ + OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. + problem: the extension of the tmp files is unusable for test generation. + unfortunately the extensions used in the DIFF lines are not always usable for the CLI + (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) + this function replaces the tmp file by the expected file. + """ + cmd = shlex.split(line) + for i, e in enumerate(cmd): + if e in diff_pairs: + dst = os.path.join("test-data", diff_pairs[e]) + if os.path.exists(dst): + os.unlink(dst) + sys.stderr.write(f"symlink {e} {dst}\n") + os.symlink(e, dst) + cmd[i] = diff_pairs[e] + return shlex.join(cmd) + + +def get_ini(line: str, tool_id: str) -> Tuple[str, str]: + """ + if there is an ini file then we use this to generate the test + otherwise the ctd file is used + other command line parameters are inserted later into this xml + """ + cmd = shlex.split(line) + ini = None + for i, e in enumerate(cmd): + if e == "-ini": + ini = cmd[i + 1] + cmd = cmd[:i] + cmd[i + 2:] + if ini: + return os.path.join("test-data", ini), shlex.join(cmd) + else: + return os.path.join("ctd", f"{tool_id}.ctd"), line + + +def unique_files(line: str): + """ + some tests use the same file twice which does not work in planemo tests + hence we create symlinks for each file used twice + """ + cmd = shlex.split(line) + # print(f"{cmd}") + files = {} + # determine the list of indexes where each file argument (anything appearing in test-data/) appears + for idx, e in enumerate(cmd): + p = os.path.join("test-data", e) + if not os.path.exists(p) and not os.path.islink(p): + continue + try: + files[e].append(idx) + except KeyError: + files[e] = [idx] + # print(f"{files=}") + for f in files: + if len(files[f]) < 2: + continue + for i, idx in enumerate(files[f]): + f_parts = f.split(".") + f_parts[0] = f"{f_parts[0]}_{i}" + new_f = ".".join(f_parts) + # if os.path.exists(os.path.join("test-data", new_f)): + # os.unlink(os.path.join("test-data", new_f)) + sys.stderr.write( + f'\tsymlink {os.path.join("test-data", new_f)} {f}\n' + ) + try: + os.symlink(f, os.path.join("test-data", new_f)) + except FileExistsError: + pass + cmd[idx] = new_f + return shlex.join(cmd) + + +def fill_ctd_clargs(ini: str, line: str, ctd_tmp: TextIO) -> None: + cmd = shlex.split(line) + + # load CTDModel + ini_model = None + try: + ini_model = CTDModel(from_file=ini) + except ModelTypeError: + pass + try: + ini_model = Parameters(from_file=ini) + except ModelTypeError: + pass + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % ( + args.ini_file + ) + + # get a dictionary of the ctd arguments where the values of the parameters + # given on the command line are overwritten + ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True) + ini_model.write_ctd(ctd_tmp, ini_values) + + +def process_test_line( + id: str, + line: str, + failing_tests: List[str], + skip_list: List[str], + diff_pairs: Dict[str, str], +) -> Optional[str]: + + re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)") + re_id_out_test = re.compile(r"_out_?[0-9]?") + + # TODO auto extract from set(OLD_OSW_PARAM ... lin + line = line.replace( + "${OLD_OSW_PARAM}", + " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false", + ) + + line = line.replace("${TOPP_BIN_PATH}/", "") + line = line.replace("${DATA_DIR_TOPP}/", "") + line = line.replace("THIRDPARTY/", "") + line = line.replace("${DATA_DIR_SHARE}/", "") + # IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differently + line = line.replace("${TMP_RIP_PATH}/", "") + # some input files are originally in a subdir (degenerated cases/), but not in test-data + line = line.replace("degenerate_cases/", "") + # determine the test and tool ids and remove the 1) add_test("TESTID" 2) trailing ) + match = re_test_id.match(line) + if not match: + sys.exit(f"Ill formated test line {line}\n") + test_id = match.group(1) + tool_id = match.group(2) + + line = f"{match.group(2)} {match.group(3)}" + + if test_id in failing_tests: + sys.stderr.write(f" skip failing {test_id} {line}\n") + return + + if id != tool_id: + sys.stderr.write(f" skip {test_id} ({id} != {tool_id}) {line}\n") + return + + if re_id_out_test.search(test_id): + sys.stderr.write(f" skip {test_id} {line}\n") + return + + for skip in skip_list: + if re.search(skip, line): + return + if re.search(skip, test_id): + return + + line = fix_tmp_files(line, diff_pairs) + # print(f"fix {line=}") + line = unique_files(line) + # print(f"unq {line=}") + ini, line = get_ini(line, tool_id) + + from dataclasses import dataclass, field + + @dataclass + class CTDConverterArgs: + input_files: list + output_destination: str + default_executable_path: Optional[str] = None + hardcoded_parameters: Optional[str] = None + parameter_hardcoder: Optional[ParameterHardcoder] = None + xsd_location: Optional[str] = None + formats_file: Optional[str] = None + add_to_command_line: str = "" + required_tools_file: Optional[str] = None + skip_tools_file: Optional[str] = None + macros_files: Optional[List[str]] = field(default_factory=list) + test_macros_files: Optional[List[str]] = field(default_factory=list) + test_macros_prefix: Optional[List[str]] = field(default_factory=list) + test_test: bool = False + test_only: bool = False + test_unsniffable: Optional[List[str]] = field(default_factory=list) + test_condition: Optional[List[str]] = ("compare=sim_size", "delta_frac=0.05") + tool_version: str = None + tool_profile: str = None + bump_file: str = None + + # create an ini/ctd file where the values are equal to the arguments from the command line + # and transform it to xml + test = [f"<!-- {test_id} -->\n"] + with tempfile.NamedTemporaryFile( + mode="w+", delete_on_close=False + ) as ctd_tmp, tempfile.NamedTemporaryFile( + mode="w+", delete_on_close=False + ) as xml_tmp: + fill_ctd_clargs(ini, line, ctd_tmp) + ctd_tmp.close() + xml_tmp.close() + parsed_ctd = parse_input_ctds(None, [ctd_tmp.name], xml_tmp.name, "xml") + ctd_args = CTDConverterArgs( + input_files=[ctd_tmp.name], + output_destination=xml_tmp.name, + macros_files=["macros.xml"], + skip_tools_file="aux/tools_blacklist.txt", + formats_file="aux/filetypes.txt", + # tool_conf_destination = "tool.conf", + hardcoded_parameters="aux/hardcoded_params.json", + tool_version="3.1", + test_only=True, + test_unsniffable=[ + "csv", + "tsv", + "txt", + "dta", + "dta2d", + "edta", + "mrm", + "splib", + ], + test_condition=["compare=sim_size", "delta_frac=0.7"], + ) + ctd_args.parameter_hardcoder = parse_hardcoded_parameters( + ctd_args.hardcoded_parameters + ) + convert_models(ctd_args, parsed_ctd) + xml_tmp = open(xml_tmp.name, "r") + for l in xml_tmp: + test.append(l) + + return "".join(test) + + +parser = argparse.ArgumentParser(description="Create Galaxy tests for a OpenMS tools") +parser.add_argument("--id", dest="id", help="tool id") +parser.add_argument("--cmake", nargs="+", help="OpenMS test CMake files") +args = parser.parse_args() +sys.stderr.write(f"generate tests for {args.id}\n") + +re_comment = re.compile("#.*") +re_empty_prefix = re.compile(r"^\s*") +re_empty_suffix = re.compile(r"\s*$") +re_add_test = re.compile(r"add_test\(\"(TOPP|UTILS)_.*/" + args.id) +re_diff = re.compile(r"\$\{DIFF\}.* -in1 ([^ ]+) -in2 ([^ ]+)") +failing_tests = get_failing_tests(args.cmake) +tests = [] + +# process the given CMake files and compile lists of +# - test lines .. essentially add_test(...) +# - and pairs of files that are diffed +jline = "" +test_lines = [] +diff_pairs = {} +for cmake in args.cmake: + with open(cmake) as cmake_fh: + for line in cmake_fh: + # remove comments, empty prefixes and suffixes + line = re_comment.sub("", line) + line = re_empty_prefix.sub("", line) + line = re_empty_suffix.sub("", line) + # skip empty lines + if line == "": + continue + + # join test statements that are split over multiple lines + if line.endswith(")"): + jline += " " + line[:-1] + else: + jline = line + continue + line, jline = jline.strip(), "" + match = re_diff.search(line) + if match: + in1 = match.group(1).split("/")[-1] + in2 = match.group(2).split("/")[-1] + if in1 != in2: + diff_pairs[in1] = in2 + elif re_add_test.match(line): + test_lines.append(line) + +for line in test_lines: + test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs) + if test: + tests.append(test) + +tests = "\n".join(tests) +print( + f""" +<xml name="autotest_{args.id}"> +{tests} +</xml> +""" +)
--- a/macros.xml Thu Dec 01 19:05:24 2022 +0000 +++ b/macros.xml Fri Jun 14 21:28:16 2024 +0000 @@ -3,19 +3,19 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.8</token> + <token name="@TOOL_VERSION@">3.1</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@TEST_DATA_LOCATION@"/> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.1.9">omssa</requirement> - <requirement type="package" version="2.13.0">blast</requirement> + <requirement type="package" version="2.14.1">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> - <requirement type="package" version="1.4">ctdopts</requirement> + <requirement type="package" version="1.5">ctdopts</requirement> <yield/> </requirements> </xml> @@ -26,6 +26,8 @@ <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> + <regex match="OMSSA ran out of RAM" level="fatal_oom" description="Could not allocate memory"/> + <regex match="comet' crashed hard (segfault-like). Please check the log." level="fatal_oom" description="Could not allocate memory"/> </stdio> </xml> <xml name="references"> @@ -113,11 +115,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'} #return m[g] #end def ]]></token></macros>
--- a/prepare_test_data_manual.sh Thu Dec 01 19:05:24 2022 +0000 +++ b/prepare_test_data_manual.sh Fri Jun 14 21:28:16 2024 +0000 @@ -1,8 +1,3 @@ -MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -13,8 +8,7 @@ CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +# TODO DeMeanderize # TODO DigestorMotif @@ -30,26 +24,17 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -FFEval -test -in FeatureFinderCentroided_1_output.featureXML -truth FeatureFinderCentroided_1_output.featureXML -out FFEval.featureXML -out_roc FFEval_roc.csv > FFEval.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - # TODO? deprecated IDDecoyProbability IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides 1 -out IDExtractor.idXML > IDExtractor.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -LabeledEval -test -in FeatureLinkerLabeled_1_input.featureXML -truth FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -68,20 +53,6 @@ OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -# adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719 -FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -#PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ - # TODO PhosphoScoring PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -118,9 +89,6 @@ RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -152,13 +120,8 @@ SpectraFilterThresholdMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr +SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML -algorithm:average_gaussian:ms_level 2 > SpectraMerger.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -# TODO SvmTheoreticalSpectrumGeneratorTrainer - -TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Thu Dec 01 19:05:24 2022 +0000 +++ b/readme.md Fri Jun 14 21:28:16 2024 +0000 @@ -11,7 +11,7 @@ * https://www.openms.de/ The wrappers for these tools and most of their tests are automatically -generated using the `generate.sh` script. The generation of the tools is +generated using the `./aux/generate.sh` script. The generation of the tools is based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter) which can be fine tuned via the `hardcoded_params.json` file. This file allows to blacklist and hardcode parameters and to modify or set arbitrary @@ -129,15 +129,6 @@ Open problems ============= -Some tools stall in CI testing using `--biocontainers` which is why the OpenMS -tools are currently listed in `.tt_biocontainer_skip`. This is - -- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius) -- OMSSAAdapter - -Using `docker -t` seems to solve the problem (see -https://github.com/galaxyproject/galaxy/issues/10153). - Licence (MIT) =============
--- a/test-data.sh Thu Dec 01 19:05:24 2022 +0000 +++ b/test-data.sh Fri Jun 14 21:28:16 2024 +0000 @@ -1,11 +1,10 @@ #!/usr/bin/env bash -VERSION=2.8 +# set -x + +VERSION=3.1 FILETYPES="aux/filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" - -# import the magic -. ./generate-foo.sh +CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2" # install conda if [ -z "$tmp" ]; then @@ -45,17 +44,20 @@ echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then - # TODO >2.8 reenable original release branch .. also in else branch - # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917 - # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT - git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT - cd $OPENMSGIT - git submodule init - git submodule update - cd - + if [[ "$created" == "yes" ]]; then + GIT_DIR=$(mktemp -d --dry-run) + GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR" + fi + git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT + ## save some space by just keeping the needed binaries + find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete + find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete + if [[ "$created" == "yes" ]]; then + rm -rf $GIT_DIR + fi else cd $OPENMSGIT - git pull origin release/$VERSION.0-plus + git pull origin release/$VERSION.0 cd - fi @@ -65,7 +67,7 @@ if conda env list | grep "$OPENMSENV"; then true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml + conda create -y --quiet --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -101,33 +103,34 @@ conda deactivate -# ############################################################################### -# ## copy all the test data files to test-data -# ## most of it (outputs) will be overwritten later, but its needed for -# ## prepare_test_data -# ############################################################################### +# # ############################################################################### +# # ## copy all the test data files to test-data +# # ## most of it (outputs) will be overwritten later, but its needed for +# # ## prepare_test_data +# # ############################################################################### echo "Get test data" -find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then - wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + wget -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML + # wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv -if [ ! -d test-data/pepnovo_models/ ]; then - mkdir -p /tmp/pepnovo - wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip PepNovo.20120423.zip -d /tmp/pepnovo/ - mv /tmp/pepnovo/Models test-data/pepnovo_models/ - rm PepNovo.20120423.zip - rm -rf /tmp/pepnovo -fi +# if [ ! -d test-data/pepnovo_models/ ]; then +# mkdir -p /tmp/pepnovo +# wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip +# unzip PepNovo.20120423.zip -d /tmp/pepnovo/ +# mv /tmp/pepnovo/Models test-data/pepnovo_models/ +# rm PepNovo.20120423.zip +# rm -rf /tmp/pepnovo +# fi ############################################################################### ## generate ctd files using the binaries in the conda package ############################################################################### @@ -170,6 +173,47 @@ ############################################################################### ## create script to create results for the tests and run it ############################################################################### +# parse data preparation calls from OpenMS sources for a tool with a given id +function prepare_test_data { +# id=$1 +# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" + + OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g') + # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | + sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" | + grep -v "\.ini\.json" | + sed 's/.ini.json /ini /' | + sed 's/#.*$//'| + sed 's/^\s*//; s/\s*$//' | + grep -v "^$" | + awk '{printf("%s@NEWLINE@", $0)}' | + sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | + sed 's/degenerate_cases\///' | + egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | + grep add_test | + egrep "TOPP|UTILS" | + sed 's@${DATA_DIR_SHARE}/@@g;'| + sed 's@${TMP_RIP_PATH}@./@g'| + sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + while read line + do + test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) + + if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then + >&2 echo " skip failing "$test_id + continue + fi + + line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) + # line="$(fix_tmp_files $line)" + echo 'echo executing "'$test_id'"' + echo "$line > $test_id.stdout 2> $test_id.stderr" + echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" + done +} + echo "Create test shell script" echo -n "" > prepare_test_data.sh @@ -180,31 +224,19 @@ echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh -echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh +echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh -echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh +echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -## prepare_test_data > tmp_test_data.sh -## # remove calls not needed for the tools listed in any .list file -## echo LIST $LIST -## if [ ! -z "$LIST" ]; then -## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -## else -## REX=".*" -## fi -## echo REX $REX -## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -## rm tmp_test_data.sh - echo "Execute test shell script" chmod u+x prepare_test_data.sh cd ./test-data || exit @@ -234,14 +266,11 @@ for i in $(ls ctd/*ctd) do b=$(basename "$i" .ctd) - get_tests2 "$b" >> "$autotests" + ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests" + wc -l "$autotests" done echo "</macros>" >> "$autotests" -# echo "Create test data links" -# Breaks DecoyDatabase -# link_tmp_files - # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests @@ -255,6 +284,7 @@ # # not able to specify composite test data # -> SpectraSTSearchAdapter +echo "Discard some tests" if [[ ! -z "$1" ]]; then echo "" > macros_discarded_auto.xml for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter @@ -272,7 +302,7 @@ ## remove broken symlinks in test-data find test-data/ -xtype l -delete -if [ ! -z "$created" ]; then +if [[ "$created" == "yes" ]]; then echo "Removing temporary directory" rm -rf "$tmp" fi