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Commit message:
Initial upload |
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README.rst proteomics_novel_peptide_filter_workflow.ga repository_dependencies.xml |
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| diff -r 000000000000 -r cb2a42d4a5ac README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Mar 17 15:55:58 2014 -0500 |
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| @@ -0,0 +1,46 @@ +This package contains a Galaxy workflow that determines if peptides identified from MS searches are present in the reference proteome. +Tool also allows for peptide annotation, for each novel peptide, by retrieving accession headers for those polypeptide sequences that exactly match the novel peptide. + +See http://www.galaxyproject.org for information about the Galaxy Project. + + +Availability +============ + +This workflow is available to download and/or install from the main +Galaxy Tool Shed: + +http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_novel_peptide_filter_workflow + + +Reference Data +============== + +For Human RNAseq data this workflow was tested using reference data from: + +* ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz + + +For Mouse RNAseq data this workflow was tested using reference data from: + +* ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + +* http://toolshed.g2.bx.psu.edu/view//jjohnson/find_in_reference + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial release to Tool Shed (March, 2014) +======= ====================================================================== + + |
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| diff -r 000000000000 -r cb2a42d4a5ac proteomics_novel_peptide_filter_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomics_novel_peptide_filter_workflow.ga Mon Mar 17 15:55:58 2014 -0500 |
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| b'@@ -0,0 +1,213 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "Example Novel Peptide Filter", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Ensembl pep.all (Reference Protein FASTA file)"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 311\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Ensembl pep.all (Reference Protein FASTA file)\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "cRAP database of MS contaminants"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 199, \n+ "top": 407\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, 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\n+ "top": 311\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "cat1", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\\\\"\\", \\"queries\\": \\"[{\\\\\\"input2\\\\\\": null, \\\\\\"__index__\\\\\\": 0}]\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "4": {\n+ "annotation": "", \n+ "id": 4, \n+ "input_connections": {\n+ "input": {\n+ "id": 3, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "FASTA-to-Tabular", \n+ "outputs": [\n+ {\n+ "name": "'..b'du/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null}", \n+ "tool_version": "1.1.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "5": {\n+ "annotation": "", \n+ "id": 5, \n+ "input_connections": {\n+ "input": {\n+ "id": 2, \n+ "output_name": "output"\n+ }, \n+ "reference": {\n+ "id": 4, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "find in reference", \n+ "outputs": [\n+ {\n+ "name": "found", \n+ "type": "tabular"\n+ }, \n+ {\n+ "name": "novel", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 898, \n+ "top": 180\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/find_in_reference/find_in_reference/0.0.1", \n+ "tool_state": "{\\"__page__\\": 0, \\"reference\\": \\"null\\", \\"column\\": \\"{\\\\\\"set\\\\\\": \\\\\\"yes\\\\\\", \\\\\\"reference_column\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"2\\\\\\"}, \\\\\\"input_column\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"2\\\\\\"}, \\\\\\"__current_case__\\\\\\": 1}\\", \\"outputs\\": \\"\\\\\\"novel\\\\\\"\\", \\"case_insensitive\\": \\"\\\\\\"True\\\\\\"\\", \\"annotate\\": \\"{\\\\\\"from_ref\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"input\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null}", \n+ "tool_version": "0.0.1", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "6": {\n+ "annotation": "", \n+ "id": 6, \n+ "input_connections": {\n+ "input": {\n+ "id": 5, \n+ "output_name": "novel"\n+ }, \n+ "reference": {\n+ "id": 4, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "find in reference", \n+ "outputs": [\n+ {\n+ "name": "found", \n+ "type": "tabular"\n+ }, \n+ {\n+ "name": "novel", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 1129, \n+ "top": 295\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/find_in_reference/find_in_reference/0.0.1", \n+ "tool_state": "{\\"__page__\\": 0, \\"reference\\": \\"null\\", \\"column\\": \\"{\\\\\\"set\\\\\\": \\\\\\"yes\\\\\\", \\\\\\"reference_column\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"2\\\\\\"}, \\\\\\"input_column\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"2\\\\\\"}, \\\\\\"__current_case__\\\\\\": 1}\\", \\"outputs\\": \\"\\\\\\"found\\\\\\"\\", \\"case_insensitive\\": \\"\\\\\\"True\\\\\\"\\", \\"annotate\\": \\"{\\\\\\"annotation_col_sep\\\\\\": \\\\\\",\\\\\\", \\\\\\"annotation_separator\\\\\\": \\\\\\";\\\\\\", \\\\\\"from_ref\\\\\\": \\\\\\"yes\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"annotation_columns\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": [\\\\\\"1\\\\\\"]}}\\", \\"input\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null}", \n+ "tool_version": "0.0.1", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r cb2a42d4a5ac repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 17 15:55:58 2014 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required tools for proteomics_rnaseq_splice_db_workflow"> + <repository name="find_in_reference" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="e7e56b51d156" /> +</repositories> |