| Previous changeset 0:05ab719b9b93 (2016-05-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/asms_tutorial_2016 commit 16fc7b82dcada630bb8eba892679d46041e0efbb-dirty |
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modified:
repository_dependencies.xml |
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added:
PeptideShaker_Identifcation_from_mzML.ga |
| b |
| diff -r 05ab719b9b93 -r 673718067538 PeptideShaker_Identifcation_from_mzML.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PeptideShaker_Identifcation_from_mzML.ga Mon May 16 09:16:49 2016 -0400 |
| [ |
| b'@@ -0,0 +1,463 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "Workflow 1 for ASMS 2016 Workshop", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Protein Database Downloader", \n+ "outputs": [\n+ {\n+ "name": "output_database", \n+ "type": "fasta"\n+ }\n+ ], \n+ "position": {\n+ "left": 245.5, \n+ "top": 147\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", \n+ "tool_state": "{\\"source\\": \\"{\\\\\\"set\\\\\\": \\\\\\"+keyword%3a1185\\\\\\", \\\\\\"from\\\\\\": \\\\\\"uniprot\\\\\\", \\\\\\"taxon\\\\\\": \\\\\\"10090\\\\\\", \\\\\\"reviewed\\\\\\": \\\\\\"+\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"include_isoform\\\\\\": \\\\\\"True\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n+ "tool_version": "0.2.0", \n+ "type": "tool", \n+ "uuid": "0130f0ee-1abf-4157-94b3-62e502b9c061", \n+ "workflow_outputs": [\n+ {\n+ "label": " Mouse Protein Database", \n+ "output_name": "output_database", \n+ "uuid": "50b914ea-7b4d-4d86-b890-910f9b14f7f6"\n+ }\n+ ]\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Protein Database Downloader", \n+ "outputs": [\n+ {\n+ "name": "output_database", \n+ "type": "fasta"\n+ }\n+ ], \n+ "position": {\n+ "left": 245.5, \n+ "top": 248\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionoutput_database": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_database"\n+ }, \n+ "RenameDatasetActionoutput_database": {\n+ "action_arguments": {\n+ "newname": "Contaminant Protein Database"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output_database"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.0", \n+ "tool_state": "{\\"source\\": \\"{\\\\\\"from\\\\\\": \\\\\\"cRAP\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n+ "tool_version": "0.2.0", \n+ "type": "tool", \n+ "uuid": "2804e8cd-8bb1-4ffc-9dcc-3ac5e373943a", \n+ "workflow_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "From proB RNAseq SpliceDB workflow", \n+ "content_id": null, \n+ "id": 2, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "From proB RNAseq SpliceDB workflow", \n+ "name": "proB Splice Isoform Database"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 177, \n+ "top": 370\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\'..b' "left": 1343.5, \n+ "top": 285\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionmzidentML": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "mzidentML"\n+ }, \n+ "HideDatasetActionoutput_certificate": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_certificate"\n+ }, \n+ "HideDatasetActionoutput_cps": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_cps"\n+ }, \n+ "HideDatasetActionoutput_hierarchical": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_hierarchical"\n+ }, \n+ "HideDatasetActionoutput_peptides": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_peptides"\n+ }, \n+ "HideDatasetActionoutput_peptides_phosphorylation": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_peptides_phosphorylation"\n+ }, \n+ "HideDatasetActionoutput_proteins": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_proteins"\n+ }, \n+ "HideDatasetActionoutput_proteins_phosphorylation": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_proteins_phosphorylation"\n+ }, \n+ "HideDatasetActionoutput_psm": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_psm"\n+ }, \n+ "HideDatasetActionoutput_psm_phosphorylation": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_psm_phosphorylation"\n+ }, \n+ "HideDatasetActionoutput_zip": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_zip"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.10.0", \n+ "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\\\\\\"\\"}", \n+ "tool_version": "1.10.0", \n+ "type": "tool", \n+ "uuid": "4ed37c6f-a6a2-4e8b-ba45-620e8b66445b", \n+ "workflow_outputs": []\n+ }\n+ }, \n+ "uuid": "a3d518ca-b4fd-48ca-884e-45ca7dd027dc"\n+}\n\\ No newline at end of file\n' |
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| diff -r 05ab719b9b93 -r 673718067538 repository_dependencies.xml --- a/repository_dependencies.xml Fri May 13 09:34:49 2016 -0400 +++ b/repository_dependencies.xml Mon May 16 09:16:49 2016 -0400 |
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| @@ -7,4 +7,8 @@ <repository changeset_revision="a51980bc0ffe" name="blast_plus_remote_blastp" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="5da5dcc5e13a" name="blastxml_to_tabular_selectable" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="626658afe4cb" name="column_maker" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b39347891609" name="dbbuilder" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2904d46167da" name="fasta_merge_files_and_filter_unique_sequences" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="29e7496f3907" name="mgf_formatter" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3ef5a7dd1a36" name="peptideshaker" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |