Mercurial > repos > galaxyp > openms_psmfeatureextractor
changeset 9:047020d9012f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 173ee0ef8aa320d2f17433d6560fff05093d127e-dirty"
| author | galaxyp |
|---|---|
| date | Sat, 30 Jan 2021 11:38:47 +0000 |
| parents | 59736982ab7b |
| children | 63fea23042c4 |
| files | PSMFeatureExtractor.xml macros_discarded_auto.xml test-data/spectrast.log |
| diffstat | 3 files changed, 380 insertions(+), 24 deletions(-) [+] |
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--- a/PSMFeatureExtractor.xml Mon Dec 14 16:54:21 2020 +0000 +++ b/PSMFeatureExtractor.xml Sat Jan 30 11:38:47 2021 +0000 @@ -1,7 +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]--> -<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy1" profile="20.05"> +<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy2" profile="20.05"> <description>Computes extra features for each input PSM.</description> <macros> <token name="@EXECUTABLE@">PSMFeatureExtractor</token> @@ -34,7 +34,7 @@ #if $in ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} #else if $in_single -'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && +'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' #end if -out 'out/output.${out_type}'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_discarded_auto.xml Sat Jan 30 11:38:47 2021 +0000 @@ -0,0 +1,378 @@ + +<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>
--- a/test-data/spectrast.log Mon Dec 14 16:54:21 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds.. - -END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -========== -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds.. - -END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -==========