Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer
diff macros_discarded_auto.xml @ 13:3c5de1c6c08a draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:21:45 +0000 |
| parents | d351b67b5317 |
| children |
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--- a/macros_discarded_auto.xml Fri Nov 06 20:02:14 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,378 +0,0 @@ - -<xml name="manutest_OpenSwathFileSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <output_collection name="outputDirectory" count=""/> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test></xml> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MSFraggerAdapter"> -<test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MaRaClusterAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="verbose" value="2"/> - <param name="precursor_tolerance" value="20.0"/> - <param name="precursor_tolerance_units" value="ppm"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/> - <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/> - <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="pcut" value="-10.0"/> - <param name="min_cluster_size" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_NovorAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NovorAdapter_in.mzML"/> - <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="enzyme" value="Trypsin"/> - <param name="fragmentation" value="CID"/> - <param name="massAnalyzer" value="Trap"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="precursor_mass_tolerance" value="15.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="variable_modifications" value="Acetyl (K)"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="forbiddenResidues" value="I"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_SpectraSTSearchAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="pep.xml"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="tsv"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml>