Mercurial > repos > galaxyp > asms_tutorial_2016
view PeptideShaker_Identifcation_from_mzML.ga @ 1:673718067538 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/asms_tutorial_2016 commit 16fc7b82dcada630bb8eba892679d46041e0efbb-dirty
author | galaxyp |
---|---|
date | Mon, 16 May 2016 09:16:49 -0400 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Workflow 1 for ASMS 2016 Workshop", "steps": { "0": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Protein Database Downloader", "outputs": [ { "name": "output_database", "type": "fasta" } ], "position": { "left": 245.5, "top": 147 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", "tool_state": "{\"source\": \"{\\\"set\\\": \\\"+keyword%3a1185\\\", \\\"from\\\": \\\"uniprot\\\", \\\"taxon\\\": \\\"10090\\\", \\\"reviewed\\\": \\\"+\\\", \\\"__current_case__\\\": 0, \\\"include_isoform\\\": \\\"True\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "0.2.0", "type": "tool", "uuid": "0130f0ee-1abf-4157-94b3-62e502b9c061", "workflow_outputs": [ { "label": " Mouse Protein Database", "output_name": "output_database", "uuid": "50b914ea-7b4d-4d86-b890-910f9b14f7f6" } ] }, "1": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", "id": 1, "input_connections": {}, "inputs": [], "label": null, "name": "Protein Database Downloader", "outputs": [ { "name": "output_database", "type": "fasta" } ], "position": { "left": 245.5, "top": 248 }, "post_job_actions": { "HideDatasetActionoutput_database": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_database" }, "RenameDatasetActionoutput_database": { "action_arguments": { "newname": "Contaminant Protein Database" }, "action_type": "RenameDatasetAction", "output_name": "output_database" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", "tool_state": "{\"source\": \"{\\\"from\\\": \\\"cRAP\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "0.2.0", "type": "tool", "uuid": "2804e8cd-8bb1-4ffc-9dcc-3ac5e373943a", "workflow_outputs": [] }, "2": { "annotation": "From proB RNAseq SpliceDB workflow", "content_id": null, "id": 2, "input_connections": {}, "inputs": [ { "description": "From proB RNAseq SpliceDB workflow", "name": "proB Splice Isoform Database" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 177, "top": 370 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"proB Splice Isoform Database\"}", "tool_version": null, "type": "data_input", "uuid": "afb73119-0730-4926-b571-fc15a9fba9c5", "workflow_outputs": [] }, "3": { "annotation": "From preB RNAseq SpliceDB workflow", "content_id": null, "id": 3, "input_connections": {}, "inputs": [ { "description": "From preB RNAseq SpliceDB workflow", "name": "preB Splice Isoform Database" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 188, "top": 495 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"preB Splice Isoform Database\"}", "tool_version": null, "type": "data_input", "uuid": "1c18cd30-ba5a-4c48-9d68-151faf005b59", "workflow_outputs": [] }, "4": { "annotation": "", "content_id": null, "id": 4, "input_connections": {}, "inputs": [ { "description": "", "name": "mzML Spectrum files" } ], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 256.5, "top": 642 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"collection_type\": \"list\", \"name\": \"mzML Spectrum files\"}", "tool_version": null, "type": "data_collection_input", "uuid": "7e4ce412-2dc8-4905-959b-b765c6fe3726", "workflow_outputs": [] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", "id": 5, "input_connections": { "inputs_0|input": { "id": 2, "output_name": "output" }, "inputs_1|input": { "id": 3, "output_name": "output" } }, "inputs": [], "label": null, "name": "FASTA Merge Files and Filter Unique Sequences", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 399.5, "top": 397 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "RenameDatasetActionoutput": { "action_arguments": { "newname": "Merged Sample Splice Isoform Databases: proB + preB" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", "tool_state": "{\"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "uuid": "dcdf18e5-3d06-4a10-a717-ef0c976345e6", "workflow_outputs": [] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mgf_formatter/mgf_formatter/0.1.0", "id": 6, "input_connections": { "type|inputs": { "id": 4, "output_name": "output" } }, "inputs": [], "label": null, "name": "MGF Formatter", "outputs": [ { "name": "output", "type": "mgf" } ], "position": { "left": 612.5, "top": 609 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mgf_formatter/mgf_formatter/0.1.0", "tool_state": "{\"__page__\": 0, \"itraq_filter\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"type\": \"{\\\"input_type\\\": \\\"mzml\\\", \\\"__current_case__\\\": 0, \\\"inputs\\\": null}\", \"mgf_format\": \"\\\"DEFAULT\\\"\"}", "tool_version": "0.1.0", "type": "tool", "uuid": "52cd6753-b0e6-4631-a98f-b7962b6ddc9b", "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", "id": 7, "input_connections": { "inputs_0|input": { "id": 0, "output_name": "output_database" }, "inputs_1|input": { "id": 1, "output_name": "output_database" }, "inputs_2|input": { "id": 5, "output_name": "output" } }, "inputs": [], "label": null, "name": "FASTA Merge Files and Filter Unique Sequences", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 711.5, "top": 209 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", "tool_state": "{\"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}, {\\\"__index__\\\": 2, \\\"input\\\": null}]\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "uuid": "c138e24b-4cb8-4e40-b277-aff37cbf6ba2", "workflow_outputs": [] }, "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/2.8.0", "id": 8, "input_connections": { "input_database": { "id": 7, "output_name": "output" }, "peak_lists": { "id": 6, "output_name": "output" } }, "inputs": [], "label": null, "name": "Search GUI", "outputs": [ { "name": "searchgui_results", "type": "searchgui_archive" } ], "position": { "left": 992.5, "top": 412 }, "post_job_actions": { "HideDatasetActionsearchgui_results": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "searchgui_results" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/2.8.0", "tool_state": "{\"msgf\": \"{\\\"msgf_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"use_gene_mapping\": \"\\\"False\\\"\", \"min_charge\": \"\\\"2\\\"\", \"__page__\": 0, \"peak_lists\": \"null\", \"engines\": \"[\\\"X!Tandem\\\", \\\"MSGF\\\", \\\"OMSSA\\\", \\\"Comet\\\"]\", \"__rerun_remap_job_id__\": null, \"create_decoy\": \"\\\"True\\\"\", \"enzyme\": \"\\\"Trypsin\\\"\", \"precursor_ion_tol_units\": \"\\\"1\\\"\", \"omssa\": \"{\\\"omssa_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"precursor_ion_tol\": \"\\\"10.0\\\"\", \"variable_modifications\": \"[\\\"Oxidation of M\\\", \\\"iTRAQ 4-plex of Y\\\"]\", \"input_database\": \"null\", \"fragment_tol\": \"\\\"0.1\\\"\", \"reverse_ion\": \"\\\"y\\\"\", \"forward_ion\": \"\\\"b\\\"\", \"searchgui_advanced\": \"{\\\"searchgui_advanced_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"xtandem\": \"{\\\"xtandem_quick_acetyl\\\": \\\"False\\\", \\\"xtandem_min_peaks\\\": \\\"15\\\", \\\"xtandem_quick_pyro\\\": \\\"False\\\", \\\"xtandem_stp_bias\\\": \\\"False\\\", \\\"xtandem_advanced\\\": \\\"yes\\\", \\\"xtandem_dynamic_range\\\": \\\"100\\\", \\\"xtandem_min_prec_mass\\\": \\\"200\\\", \\\"xtandem_output_sequences\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"xtandem_output_proteins\\\": \\\"False\\\", \\\"xtandem_output_spectra\\\": \\\"True\\\", \\\"xtandem_npeaks\\\": \\\"50\\\", \\\"xtandem_noise_suppr\\\": \\\"True\\\", \\\"xtandem_min_frag_mz\\\": \\\"200\\\", \\\"xtandem_evalue\\\": \\\"100.0\\\", \\\"xtandem_refine\\\": {\\\"xtandem_refine_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}\", \"max_charge\": \"\\\"6\\\"\", \"fixed_modifications\": \"[\\\"Carbamidomethylation of C\\\", \\\"iTRAQ 4-plex of K\\\", \\\"iTRAQ 4-plex of peptide N-term\\\"]\", \"comet\": \"{\\\"comet_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"missed_cleavages\": \"\\\"2\\\"\"}", "tool_version": "2.8.0", "type": "tool", "uuid": "aaa7fa44-ab4f-4f0c-8497-235885e4e8cb", "workflow_outputs": [] }, "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.10.0", "id": 9, "input_connections": { "searchgui_input": { "id": 8, "output_name": "searchgui_results" } }, "inputs": [], "label": null, "name": "Peptide Shaker", "outputs": [ { "name": "mzidentML", "type": "mzid" }, { "name": "output_cps", "type": "peptideshaker_archive" }, { "name": "output_zip", "type": "zip" }, { "name": "output_certificate", "type": "txt" }, { "name": "output_hierarchical", "type": "tabular" }, { "name": "output_psm_phosphorylation", "type": "tabular" }, { "name": "output_psm", "type": "tabular" }, { "name": "output_peptides_phosphorylation", "type": "tabular" }, { "name": "output_peptides", "type": "tabular" }, { "name": "output_proteins_phosphorylation", "type": "tabular" }, { "name": "output_proteins", "type": "tabular" } ], "position": { "left": 1343.5, "top": 285 }, "post_job_actions": { "HideDatasetActionmzidentML": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "mzidentML" }, "HideDatasetActionoutput_certificate": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_certificate" }, "HideDatasetActionoutput_cps": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_cps" }, "HideDatasetActionoutput_hierarchical": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_hierarchical" }, "HideDatasetActionoutput_peptides": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_peptides" }, "HideDatasetActionoutput_peptides_phosphorylation": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_peptides_phosphorylation" }, "HideDatasetActionoutput_proteins": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_proteins" }, "HideDatasetActionoutput_proteins_phosphorylation": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_proteins_phosphorylation" }, "HideDatasetActionoutput_psm": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_psm" }, "HideDatasetActionoutput_psm_phosphorylation": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_psm_phosphorylation" }, "HideDatasetActionoutput_zip": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_zip" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.10.0", "tool_state": "{\"__page__\": 0, \"processing_options\": \"{\\\"processing_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"filtering_options\": \"{\\\"max_precursor_error_type\\\": \\\"1\\\", \\\"filtering_options_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"max_precursor_error\\\": \\\"10.0\\\", \\\"exclude_unknown_ptms\\\": \\\"True\\\", \\\"max_peptide_length\\\": \\\"50\\\", \\\"min_peptide_length\\\": \\\"6\\\"}\", \"searchgui_input\": \"null\", \"species_type\": \"{\\\"species_type_selector\\\": \\\"no_species_type\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"mzidentML\\\", \\\"3\\\", \\\"7\\\", \\\"0\\\"]\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", "tool_version": "1.10.0", "type": "tool", "uuid": "4ed37c6f-a6a2-4e8b-ba45-620e8b66445b", "workflow_outputs": [] } }, "uuid": "a3d518ca-b4fd-48ca-884e-45ca7dd027dc" }