Mercurial > repos > galaxyp > openms_rnpxlsearch
view macros_discarded_auto.xml @ 10:7df285ee982e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author | galaxyp |
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date | Fri, 06 Nov 2020 19:46:50 +0000 |
parents | 25cc460f9092 |
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<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>