| Next changeset 1:6066b729f9aa (2022-03-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" |
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added:
macros_modifications.xml metanovo.xml |
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| diff -r 000000000000 -r 9025f297a511 macros_modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_modifications.xml Tue Mar 29 16:54:19 2022 +0000 |
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| b'@@ -0,0 +1,294 @@\n+<macros>\n+ <!-- Although the options for fixed and variable modifications are the same, two macros are used to set different default options -->\n+ <xml name="fixed_modifications">\n+ <option value="18O(1) of peptide C-term">18O(1) of peptide C-term</option>\n+ <option value="18O(2) of peptide C-term">18O(2) of peptide C-term</option>\n+ <option value="4-Hydroxyproline">4-Hydroxyproline</option>\n+ <option value="Acetaldehyde +26">Acetaldehyde +26</option>\n+ <option value="Acetylation of K">Acetylation of K</option>\n+ <option value="Acetylation of peptide N-term">Acetylation of peptide N-term</option>\n+ <option value="Acetylation of protein N-term">Acetylation of protein N-term</option>\n+ <option value="Amidation of the peptide C-term">Amidation of the peptide C-term</option>\n+ <option value="Amidation of the protein C-term">Amidation of the protein C-term</option>\n+ <option value="Arginine 13C(6)">Arginine 13C(6)</option>\n+ <option value="Arginine 13C(6) 15N(4)">Arginine 13C(6) 15N(4)</option>\n+ <option value="Carbamidomethylation of C" selected="true">Carbamidomethylation of C</option>\n+ <option value="Carbamidomethylation of E">Carbamidomethylation of E</option>\n+ <option value="Carbamidomethylation of K">Carbamidomethylation of K</option>\n+ <option value="Carbamilation of K">Carbamilation of K</option>\n+ <option value="Carbamilation of protein N-term">Carbamilation of protein N-term</option>\n+ <option value="Carboxymethylation of C">Carboxymethylation of C</option>\n+ <option value="Citrullination of R">Citrullination of R</option>\n+ <option value="Deamidation of N">Deamidation of N</option>\n+ <option value="Deamidation of N 18O">Deamidation of N 18O</option>\n+ <option value="Deamidation of Q">Deamidation of Q</option>\n+ <option value="Dehydration of S">Dehydration of S</option>\n+ <option value="Dehydration of T">Dehydration of T</option>\n+ <option value="Didehydro of T">Didehydro of T</option>\n+ <option value="Diiodination of Y">Diiodination of Y</option>\n+ <option value="Dimethylation of K">Dimethylation of K</option>\n+ <option value="Dimethylation of K 2H(4)">Dimethylation of K 2H(4)</option>\n+ <option value="Dimethylation of K 2H(6)">Dimethylation of K 2H(6)</option>\n+ <option value="Dimethylation of K 2H(6) 13C(2)">Dimethylation of K 2H(6) 13C(2)</option>\n+ <option value="Dimethylation of R">Dimethylation of R</option>\n+ <option value="Dimethylation of peptide N-term">Dimethylation of peptide N-term</option>\n+ <option value="Dimethylation of peptide N-term 2H(4)">Dimethylation of peptide N-term 2H(4)</option>\n+ <option value="Dimethylation of peptide N-term 2H(6)">Dimethylation of peptide N-term 2H(6)</option>\n+ <option value="Dimethylation of peptide N-term 2H(6) 13C(2)">Dimethylation of peptide N-term 2H(6) 13C(2)</option>\n+ <option value="Dioxidation of M">Dioxidation of M</option>\n+ <option value="Dioxidation of W">Dioxidation of W</option>\n+ <option value="Farnesylation of C">Farnesylation of C</option>\n+ <option value="FormylMet of protein N-term">FormylMet of protein N-term</option>\n+ <option value="Formylation of K">Formylation of K</option>\n+ <option value="Formylation of S">Formylation of S</option>\n+ <option value="Formylation of T">Formylation of T</option>\n+ <option value="Formylation of peptide N-term">Formylation of peptide N-term</option>\n+ <option value="Formylation of protein N-term">Formylation of protein N-term</option>\n+ <option value="Geranyl-geranyl of C">Geranyl-geranyl of C</option>\n+ <option value="Glutathione of C">Glutathione of C</option>\n+ <option value="Guanidination of K">Guanidination of K</option>\n+ <option value="Guanidination of peptide N-term">Guanidination of peptide N-term</option>\n+ <option value="Hex(1)NAc(1) of S">Hex(1)NAc(1) of S</option>\n+ <option value="Hex(1)NAc(1) of T">Hex(1)NAc(1) of T</option>\n+ <option v'..b'option value="Palmitoylation of protein N-term">Palmitoylation of protein N-term</option>\n+ <option value="Phosphorylation of S">Phosphorylation of S</option>\n+ <option value="Phosphorylation of T">Phosphorylation of T</option>\n+ <option value="Phosphorylation of Y">Phosphorylation of Y</option>\n+ <option value="Proline 13C(5)">Proline 13C(5)</option>\n+ <option value="Propionamide of C">Propionamide of C</option>\n+ <option value="Propionamide of K">Propionamide of K</option>\n+ <option value="Propionamide of peptide N-term">Propionamide of peptide N-term</option>\n+ <option value="Propionyl of K heavy">Propionyl of K heavy</option>\n+ <option value="Propionyl of K light">Propionyl of K light</option>\n+ <option value="Propionyl of peptide N-term heavy">Propionyl of peptide N-term heavy</option>\n+ <option value="Propionyl of peptide N-term light">Propionyl of peptide N-term light</option>\n+ <option value="Pyridylethyl of C">Pyridylethyl of C</option>\n+ <option value="Pyrolidone from E">Pyrolidone from E</option>\n+ <option value="Pyrolidone from Q">Pyrolidone from Q</option>\n+ <option value="Pyrolidone from carbamidomethylated C">Pyrolidone from carbamidomethylated C</option>\n+ <option value="SUMO-2/3 Q87R">SUMO-2/3 Q87R</option>\n+ <option value="Sodium adduct to D">Sodium adduct to D</option>\n+ <option value="Sodium adduct to E">Sodium adduct to E</option>\n+ <option value="Sulfation of S">Sulfation of S</option>\n+ <option value="Sulfation of T">Sulfation of T</option>\n+ <option value="Sulfation of Y">Sulfation of Y</option>\n+ <option value="TMT 10-plex of K">TMT 10-plex of K</option>\n+ <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>\n+ <option value="TMT 2-plex of K">TMT 2-plex of K</option>\n+ <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>\n+ <option value="TMT 6-plex of K">TMT 6-plex of K</option>\n+ <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>\n+ <option value="Thioacyl of peptide N-term">Thioacyl of peptide N-term</option>\n+ <option value="Trideuterated Methyl Ester of D">Trideuterated Methyl Ester of D</option>\n+ <option value="Trideuterated Methyl Ester of E">Trideuterated Methyl Ester of E</option>\n+ <option value="Trideuterated Methyl Ester of K">Trideuterated Methyl Ester of K</option>\n+ <option value="Trideuterated Methyl Ester of R">Trideuterated Methyl Ester of R</option>\n+ <option value="Trideuterated Methyl Ester of peptide C-term">Trideuterated Methyl Ester of peptide C-term</option>\n+ <option value="Trimethylation of K">Trimethylation of K</option>\n+ <option value="Trimethylation of R">Trimethylation of R</option>\n+ <option value="Trimethylation of protein N-term A">Trimethylation of protein N-term A</option>\n+ <option value="Trioxidation of C">Trioxidation of C</option>\n+ <option value="Ubiquitination of K">Ubiquitination of K</option>\n+ <option value="iTRAQ 4-plex of K">iTRAQ 4-plex of K</option>\n+ <option value="iTRAQ 4-plex of Y">iTRAQ 4-plex of Y</option>\n+ <option value="iTRAQ 4-plex of peptide N-term">iTRAQ 4-plex of peptide N-term</option>\n+ <option value="iTRAQ 8-plex of K">iTRAQ 8-plex of K</option>\n+ <option value="iTRAQ 8-plex of Y">iTRAQ 8-plex of Y</option>\n+ <option value="iTRAQ 8-plex of peptide N-term">iTRAQ 8-plex of peptide N-term</option>\n+ <option value="mTRAQ of 13C(6) 15N(2)">mTRAQ of 13C(6) 15N(2)</option>\n+ <option value="mTRAQ of K 13C(3) 15N">mTRAQ of K 13C(3) 15N</option>\n+ <option value="mTRAQ of K light">mTRAQ of K light</option>\n+ <option value="mTRAQ of peptide N-term 13C(3) 15N">mTRAQ of peptide N-term 13C(3) 15N</option>\n+ <option value="mTRAQ of peptide N-term 13C(6) 15N(2)">mTRAQ of peptide N-term 13C(6) 15N(2)</option>\n+ <option value="mTRAQ of peptide N-term light">mTRAQ of peptide N-term light</option>\n+ </xml>\n+</macros>\n+\n' |
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| diff -r 000000000000 -r 9025f297a511 metanovo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metanovo.xml Tue Mar 29 16:54:19 2022 +0000 |
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| b'@@ -0,0 +1,339 @@\n+<tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy0" profile="20.09">\n+ <description>\n+ Produce targeted databases for mass spectrometry analysis.\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>\n+ </requirements>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.9.4</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@SUBSTITUTION_RX@">[^\\w\\-\\.]</token>\n+ <import>macros_modifications.xml</import>\n+ </macros>\n+ <command>\n+ <![CDATA[\n+ #set $mgf_dir = \'mgf_files\'\n+ #set $fasta_dir = \'fasta_file\'\n+ #set fasta_name = re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($input_fasta.element_identifier))\n+ mkdir $mgf_dir &&\n+ mkdir $fasta_dir &&\n+ ln -s \'$input_fasta\' \'$fasta_dir/$fasta_name\' &&\n+\n+ #if $input_type.type == "collection"\n+ #set mgf_names = [re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($n.element_identifier)) for $n in $input_type.input_mgf_collection]\n+ #for $mgf_name in $mgf_names:\n+ ln -s \'$input\' \'$mgf_dir/$mgf_name\' &&\n+ #end for\n+ #else\n+ #set mgf_name = re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($input_type.input_mgf.element_identifier))\n+ ln -s \'$input_mgf\' \'$mgf_dir/$mgf_name\' &&\n+ #end if\n+\n+ cat $metanovo_config > config.sh &&\n+ metanovo.sh config.sh\n+ ]]>\n+ </command>\n+\n+ <configfiles>\n+ <configfile name="metanovo_config"><![CDATA[#slurp\n+#import re\n+MGF_FOLDER=mgf_files\n+#set fasta_name = re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($input_fasta.element_identifier))\n+FASTA_FILE=fasta_file/\'$fasta_name\'\n+OUTPUT_FOLDER=.\n+CHUNKSIZE=$processing_control.CHUNKSIZE\n+THREAD_LIMIT=$processing_control.THREAD_LIMIT\n+JVM_Xmx=\'$processing_control.JVM_Xmx\'\n+JVM_Xms=\'$processing_control.JVM_Xms\'\n+mn_specificity=\'$metanovo_parameters.mn_specificity\'\n+mn_enzymes=\'$metanovo_parameters.mn_enzymes\'\n+mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages\n+dg_pepnovo=0\n+dg_pnovo=0\n+dg_novor=0\n+dg_directag=1\n+prec_tol=$spectrum_matching_parameters.prec_tol\n+prec_ppm=$spectrum_matching_parameters.prec_ppm\n+frag_tol=$spectrum_matching_parameters.frag_tol\n+frag_ppm=$spectrum_matching_parameters.frag_ppm\n+digestion=$spectrum_matching_parameters.digestion\n+enzyme=\'$spectrum_matching_parameters.enzyme\'\n+specificity=$spectrum_matching_parameters.specificity\n+mc=\'$spectrum_matching_parameters.mc\'\n+fixed_mods="$spectrum_matching_parameters.fixed_mods"\n+variable_mods="$spectrum_matching_parameters.variable_mods"\n+min_charge=$spectrum_matching_parameters.min_charge\n+max_charge=$spectrum_matching_parameters.max_charge\n+fi=\'$spectrum_matching_parameters.fi\'\n+ri=\'$spectrum_matching_parameters.ri\'\n+min_isotope=\'$spectrum_matching_parameters.min_isotope\'\n+max_isotope=\'$spectrum_matching_parameters.max_isotope\'\n+annotation_level=$spectrum_annotation.annotation_level\n+annotation_high_resolution=$spectrum_annotation.annotation_high_resolution\n+sequence_index_type=$sequence_matching.sequence_index_type\n+sequence_matching_type=$sequence_matching.sequence_matching_type\n+sequence_matching_x=$sequence_matching.sequence_matching_x\n+import_peptide_length_min=$import_filters.import_peptide_length_min\n+import_peptide_length_max=$import_filters.import_peptide_length_max\n+import_precursor_mz_ppm=$import_filters.import_precursor_mz_ppm\n+exclude_unknown_ptms=$import_filters.exclude_unknown_ptms\n+ptm_score=$ptm_localization.ptm_score\n+score_neutral_losses=$ptm_localization.score_neutral_losses\n+ptm_sequence_matching_type=$ptm_localization.ptm_sequence_matching_type\n+ptm_alignment=$ptm_localization.ptm_alignment\n+useGeneMapping=$gene_annotation.useGeneMapping\n+updateGeneMapping=$gene_annotation.updateGeneMapping\n+simplify_groups=$protein_inference.simplify_groups\n+simplify_score=$protein_inference.simplify_score\n+simplify_enzymaticity=$protein_inference.simplify_enzymaticity\n+simplify_evidence=$protein_inference.simplify_evidence\n+simplify_uncharacterized=$pro'..b'ment="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>\n+ <param name="directag_ms_charge_state" argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>\n+ <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>\n+ <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select">\n+ <option selected="true" value="0">No deisotoping</option>\n+ <option value="1">Precursor only</option>\n+ <option value="2">Precursor and candidate</option>\n+ </param>\n+ <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>\n+ <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>\n+ <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>\n+ <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>\n+ <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>\n+ <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>\n+ <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>\n+ <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="MetaNovo Output FASTA"/>\n+ <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="MetaNovo Output CSV"/>\n+ </outputs>\n+ <help><![CDATA[\n+**MetaNovo**\n+\n+MetaNovo searches MS/MS data against a FASTA database of known proteins.\n+\n+Two outputs are produced:\n+\n+- MetaNovo Output FASTA: the matching proteins produced by the search.\n+- MetaNovo Output CSV: information about the job and other useful metadata.\n+\n+Two inputs are required: an MGF file or files and a FASTA database file.\n+\n+Two different input types are available for the MGF input. The correct input configuration depends on the desired use case, as outlined below:\n+\n+======================================================= =============\n+Use case Configuration\n+======================================================= =============\n+Single input MGF file, single output FASTA file **Single file** input with **Single dataset** selected\n+Multiple input MGF files, multiple output FASTA files\\* **Single file** input with **Multiple datasets** OR **Dataset collection** selected\n+Multiple input MGF files, single output FASTA file **Collection** input\n+======================================================= =============\n+\n+**\\*** One for each MGF file.\n+\n+In the second use case, a separate MetaNovo job is spawned for each input MGF. In the third use case, a single MetaNovo job runs with all MGF files in the collection as input.\n+\n+If the third use case fails due to memory limitations, users are recommended to use the second option. The multiple output FASTA databases may be merged to generate a reduced, compact database.\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1101/605550</citation>\n+ </citations>\n+</tool>\n' |