| Next changeset 1:47db0b303a50 (2015-09-07) |
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Commit message:
first release |
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added:
SADI-Docker_use_case.ga UniProt_IDs.txt |
| b |
| diff -r 000000000000 -r 22be3a551998 SADI-Docker_use_case.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SADI-Docker_use_case.ga Fri Sep 04 23:33:16 2015 +0200 |
| [ |
| b'@@ -0,0 +1,520 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "SADI-Docker use case", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Convert", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 309, \n+ "top": 203\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "Convert characters1", \n+ "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"condense\\": \\"\\\\\\"True\\\\\\"\\", \\"__workflow_invocation_uuid__\\": \\"\\\\\\"81ac14fc519c11e59bbf5c514f7c7883\\\\\\"\\", \\"strip\\": \\"\\\\\\"True\\\\\\"\\", \\"input\\": \\"null\\", \\"convert_from\\": \\"\\\\\\"s\\\\\\"\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "658762bb-9052-4dd2-bb6b-e77613a6dcfe"\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {\n+ "input": {\n+ "id": 0, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Add column", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 304, \n+ "top": 336\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "addValue", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"__workflow_invocation_uuid__\\": \\"\\\\\\"81ac14fc519c11e59bbf5c514f7c7883\\\\\\"\\", \\"exp\\": \\"\\\\\\"http://openlifedata.org/uniprot:\\\\\\"\\", \\"iterate\\": \\"\\\\\\"no\\\\\\"\\", \\"input\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "c2421757-1d5d-435c-ac9e-fb036ccd4448"\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n+ "input_connections": {\n+ "input1": {\n+ "id": 1, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Merge Columns", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 306, \n+ "top": 474\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "mergeCols1", \n+ "tool_state": "{\\"__page__\\": 0, \\"input1\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"col2\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"1\\\\\\"}\\", \\"__workflow_invocation_uuid__\\": \\"\\\\\\"81ac14fc519c11e59bbf5c514f7c7883\\\\\\"\\", \\"col1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"2\\\\\\"}\\", \\"chromInfo\\": \\"\\\\\\"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"columns\\": \\"[]\\"}", \n+ "tool_version": "1.0.1", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "63b4d2ff-0e1d-449d-aad5-a2ccd033d36a"\n+ }, \n+ "3": {\n+ '..b' "id": 14, \n+ "input_connections": {\n+ "input_files_0|input_file": {\n+ "id": 13, \n+ "output_name": "output"\n+ }, \n+ "input_files_1|input_file": {\n+ "id": 12, \n+ "output_name": "output"\n+ }, \n+ "input_files_2|input_file": {\n+ "id": 11, \n+ "output_name": "output"\n+ }, \n+ "input_files_3|input_file": {\n+ "id": 10, \n+ "output_name": "output"\n+ }, \n+ "input_files_4|input_file": {\n+ "id": 9, \n+ "output_name": "output_file"\n+ }, \n+ "input_files_5|input_file": {\n+ "id": 8, \n+ "output_name": "output_file"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "SADI - Merge RDF Graphs", \n+ "outputs": [\n+ {\n+ "name": "output_file", \n+ "type": "rdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 1230, \n+ "top": 319\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "SADI-Docker-mergeRDFgraphs", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"chromInfo\\": \\"\\\\\\"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"input_files\\": \\"[{\\\\\\"__index__\\\\\\": 0, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 1, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 2, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 3, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 4, \\\\\\"input_file\\\\\\": null}, {\\\\\\"__index__\\\\\\": 5, \\\\\\"input_file\\\\\\": null}]\\"}", \n+ "tool_version": "0.1", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "7c24dd55-3032-4329-9fa3-734c963d8ed2"\n+ }, \n+ "15": {\n+ "annotation": "", \n+ "id": 15, \n+ "input_connections": {\n+ "ontology": {\n+ "id": 14, \n+ "output_name": "output_file"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "SADI - Execute an SPARQL query against an RDF file", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "html"\n+ }\n+ ], \n+ "position": {\n+ "left": 1544, \n+ "top": 462\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "SADI-Docker-SPARQLGalaxy", \n+ "tool_state": "{\\"out_format\\": \\"\\\\\\"html\\\\\\"\\", \\"__page__\\": 0, \\"pasted_query\\": \\"\\\\\\"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \\\\\\\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\\\\\\\nPREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#>\\\\\\\\nPREFIX lsrn: <http://purl.oclc.org/SADI/LSRN/>\\\\\\\\n\\\\\\\\nSELECT ?protein ?label ?KEGG\\\\\\\\nWHERE { \\\\\\\\n?protein rdf:type lsrn:UniProt_Record . \\\\\\\\n?protein sadi:isEncodedBy ?KEGG . \\\\\\\\n?protein ?prot2hgnc ?hgnc . \\\\\\\\n?hgnc ?hgnc2omim ?omim . \\\\\\\\n?omim ?omim2pubmed ?pubmed . \\\\\\\\n?pubmed rdfs:label ?label . \\\\\\\\nFILTER (regex (?label, \'brain\'))\\\\\\\\n}\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"ontology\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+ "tool_version": "0.1", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "9a453f8c-370e-4ab7-8e45-73cbba721db9"\n+ }\n+ }, \n+ "uuid": "8e1b472f-1048-49d0-a90a-5faeb29e70c6"\n+}\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 22be3a551998 UniProt_IDs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/UniProt_IDs.txt Fri Sep 04 23:33:16 2015 +0200 |
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| @@ -0,0 +1,200 @@ +Q03164 +Q9UKA4 +Q8TDM6 +Q9NQT8 +Q12830 +Q9HCM3 +Q8TF72 +Q5H8C1 +Q9UGU0 +B2RWN9 +A4UGR9 +B7ZML1 +F2Z2U4 +F8VPD4 +O75443 +Q9UKN7 +Q13439 +Q6RI45 +Q92608 +B2RUT2 +F8W9C3 +E9PC93 +J3KPF0 +F5H4B5 +Q9Y485 +W5ZR30 +Q5XUU0 +P51610 +Q149P0 +B5MDV5 +H7BZ55 +J3QK84 +Q92614 +J3QTQ0 +B7XCW9 +E7ENL6 +Q9P2D8 +Q9P281 +Q7Z406 +O14686 +Q09472 +Q9BX84 +Q63HN8 +Q2HXI4 +A4D1A8 +A4FU77 +Q8IZD2 +Q92538 +Q01082 +Q14686 +Q69YN4 +D6W5H5 +A7E2V4 +B0I1R8 +F8VU39 +Q9BY89 +Q9NTG1 +Q5JB40 +Q5T5U3 +O43149 +P35499 +J3KNV1 +E9PBA5 +Q9UIW2 +Q86WI1 +P49454 +Q96RT7 +Q5D862 +B7ZM61 +E9PAT2 +E9PDY4 +F8W9J4 +U3KQJ8 +P08519 +Q3ZCN5 +A6NE01 +B7ZMI1 +D3YHM4 +E7EPM4 +F5GZI5 +B1AQK6 +Q8N4C6 +Q99250 +Q8TDX9 +O60673 +Q96T58 +Q58EX2 +Q6ZR08 +Q9BZ29 +O75923 +T1R7N1 +F5H269 +Q9UKZ4 +Q7Z442 +O75643 +Q8WXH0 +Q15413 +A7Y9J9 +G3XAE2 +H0YA77 +Q99973 +Q96JB1 +P25054 +P35556 +Q5HYC2 +Q5CZC0 +F8W7S2 +Q01484 +P51587 +Q6ZS30 +E9PG32 +O15050 +Q8IZC6 +Q5VU43 +Q53TY4 +Q53SY7 +E7EUA6 +E9PEL9 +H0YGL9 +T1R7A8 +Q02388 +Q9C0F0 +Q5CZ96 +Q2WGJ9 +Q9C0D2 +Q92508 +J3KN01 +A3KMH1 +Q59GD8 +E9PNZ4 +O60287 +B0I1S1 +B7ZLH8 +E9PJ64 +F2Z2U8 +D3DT72 +Q7Z7A1 +Q96JI7 +O60229 +P17927 +Q9BYW2 +Q5JSL3 +Q96QE3 +Q13129 +B2RUT8 +F8W8Y7 +Q9UPS6 +Q9UL36 +Q6ZMW3 +Q68CT4 +D3DPG0 +E9PQ73 +H9KVB4 +G8JLL9 +Q86UQ4 +O15078 +Q15746 +Q5T1R4 +Q5VT06 +Q9P2P6 +P10586 +A7E2Y5 +A7KAX9 +B0I1R4 +E9PBJ0 +Q08E86 +I0B0K8 +Q15154 +Q9UPQ9 +Q9HC84 +D3DSQ0 +Q5VU65 +A6NKB5 +F5H619 +K9LC76 +Q03001 +P12111 +Q4LDE5 +Q70CQ2 +Q4LE79 +Q8IZX4 +R4GNB2 +T1R7Q9 +P04275 +O95996 +Q460N5 +Q8TDI0 +F8W9F9 +Q9C0G6 +Q9P2P1 +Q6N022 +Q9Y4D8 +Q59FG6 +Q9H251 +A6NIW2 +Q09666 +O00763 +Q6ZU64 +B3W695 +E7ER45 |