| Previous changeset 0:b92f5ab6d127 (2017-01-09) Next changeset 2:58c9294400ed (2017-05-12) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty |
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modified:
GeneSeqToFamily.ga GeneSeqToFamily.png finding_orphan_genes.ga finding_orphan_genes.png |
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| diff -r b92f5ab6d127 -r 267a94f068d7 GeneSeqToFamily.ga --- a/GeneSeqToFamily.ga Mon Jan 09 15:06:04 2017 -0500 +++ b/GeneSeqToFamily.ga Mon Feb 20 12:57:16 2017 -0500 |
| [ |
| b'@@ -12,19 +12,19 @@\n "inputs": [\n {\n "description": "", \n- "name": "CDS sequences"\n+ "name": "CDS"\n }\n ], \n- "label": null, \n+ "label": "CDS", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 620, \n- "top": 388.875\n+ "left": 350.0625, \n+ "top": 418.0625\n }, \n "tool_errors": null, \n "tool_id": null, \n- "tool_state": "{\\"name\\": \\"CDS sequences\\"}", \n+ "tool_state": "{\\"name\\": \\"CDS\\"}", \n "tool_version": null, \n "type": "data_input", \n "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", \n@@ -44,19 +44,19 @@\n "inputs": [\n {\n "description": "", \n- "name": "Genes"\n+ "name": "Gene feature information"\n }\n ], \n- "label": null, \n+ "label": "Gene feature information", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 612.8125, \n- "top": 1110.9375\n+ "left": 342.875, \n+ "top": 1140.125\n }, \n "tool_errors": null, \n "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Genes\\"}", \n+ "tool_state": "{\\"name\\": \\"Gene feature information\\"}", \n "tool_version": null, \n "type": "data_input", \n "uuid": "3fbf4a09-9207-4a18-a133-0d865f9614f6", \n@@ -76,19 +76,19 @@\n "inputs": [\n {\n "description": "", \n- "name": "species tree"\n+ "name": "Species tree"\n }\n ], \n- "label": null, \n+ "label": "Species tree", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 605.9375, \n- "top": 1409\n+ "left": 336, \n+ "top": 1438.171875\n }, \n "tool_errors": null, \n "tool_id": null, \n- "tool_state": "{\\"name\\": \\"species tree\\"}", \n+ "tool_state": "{\\"name\\": \\"Species tree\\"}", \n "tool_version": null, \n "type": "data_input", \n "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3", \n@@ -125,8 +125,8 @@\n }\n ], \n "position": {\n- "left": 847.0625, \n- "top": 388.875\n+ "left": 577.125, \n+ "top": 418.0625\n }, \n "post_job_actions": {\n "HideDatasetActionout_file1": {\n@@ -178,8 +178,8 @@\n }\n ], \n "position": {\n- "left": 1094.1875, \n- "top": 170.8125\n+ 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"e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", \n "workflow_outputs": []\n }, \n- "14": {\n+ "13": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", \n- "id": 14, \n+ "id": 13, \n "input_connections": {\n "aln": {\n- "id": 13, \n+ "id": 12, \n "output_name": "out_file1"\n }, \n "species_tree": {\n@@ -794,8 +752,8 @@\n }\n ], \n "position": {\n- "left": 1900.9375, \n- "top": 1414.375\n+ "left": 1631, \n+ "top": 1443.5625\n }, \n "post_job_actions": {\n "HideDatasetActionoutput": {\n@@ -818,21 +776,21 @@\n "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", \n "workflow_outputs": []\n }, \n- "15": {\n+ "14": {\n "annotation": "", \n- "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", \n- "id": 15, \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", \n+ "id": 14, \n "input_connections": {\n "alignmentFile": {\n- "id": 11, \n- "output_name": "cigar"\n+ "id": 10, \n+ "output_name": "fasta_aln"\n }, \n "genesFile": {\n "id": 1, \n "output_name": "output"\n }, \n "treeFile": {\n- "id": 14, \n+ "id": 13, \n "output_name": "output"\n }\n }, \n@@ -859,20 +817,20 @@\n }\n ], \n "position": {\n- "left": 2507.9375, \n- "top": 1050.375\n+ "left": 2238, \n+ "top": 1079.5625\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", \n "tool_shed_repository": {\n- "changeset_revision": "af9f72ddf7f9", \n+ "changeset_revision": "fc8ca4ade638", \n "name": "gafa", \n "owner": "earlhaminst", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n "tool_state": "{\\"__page__\\": 0, \\"treeFile\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"alignmentFile\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"genesFile\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n- "tool_version": "0.1.0", \n+ "tool_version": "0.2.0", \n "type": "tool", \n "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", \n "workflow_outputs": [\n@@ -884,5 +842,5 @@\n ]\n }\n }, \n- "uuid": "7ae94ea4-e34a-4e09-a15c-31839c6e5eef"\n+ "uuid": "8a774cd5-046c-4272-badd-8e84aaed9c0f"\n }\n' |
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| diff -r b92f5ab6d127 -r 267a94f068d7 GeneSeqToFamily.png |
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| Binary file GeneSeqToFamily.png has changed |
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| diff -r b92f5ab6d127 -r 267a94f068d7 finding_orphan_genes.ga --- a/finding_orphan_genes.ga Mon Jan 09 15:06:04 2017 -0500 +++ b/finding_orphan_genes.ga Mon Feb 20 12:57:16 2017 -0500 |
| [ |
| b'@@ -15,12 +15,12 @@\n "name": "blast_parser data"\n }\n ], \n- "label": null, \n+ "label": "blast_parser data", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 199.94483947753906, \n- "top": 276.4521942138672\n+ "left": 199.9375, \n+ "top": 276.4375\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -47,12 +47,12 @@\n "name": "CDS"\n }\n ], \n- "label": null, \n+ "label": "CDS", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 195.93748474121094, \n- "top": 553.3639373779297\n+ "left": 195.921875, \n+ "top": 553.359375\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -69,9 +69,41 @@\n ]\n }, \n "2": {\n+ "annotation": "List of IDs discarded from hcluster_sg results", \n+ "content_id": null, \n+ "id": 2, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "List of IDs discarded from hcluster_sg results", \n+ "name": "hcluster_sg discarded"\n+ }\n+ ], \n+ "label": "hcluster_sg discarded", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 191, \n+ "top": 697\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"hcluster_sg discarded\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "3866a37f-3309-4c5d-8ed9-bb7c21d25d8a", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output", \n+ "uuid": "f9fe709d-8a1b-44b0-9989-688af44b16ad"\n+ }\n+ ]\n+ }, \n+ "3": {\n "annotation": "", \n "content_id": "Cut1", \n- "id": 2, \n+ "id": 3, \n "input_connections": {\n "input": {\n "id": 0, \n@@ -93,8 +125,8 @@\n }\n ], \n "position": {\n- "left": 429.9632110595703, \n- "top": 276.4521942138672\n+ "left": 429.953125, \n+ "top": 276.4375\n }, \n "post_job_actions": {\n "HideDatasetActionout_file1": {\n@@ -111,10 +143,10 @@\n "uuid": "3d809485-291c-4858-ade6-2f465bf667f0", \n "workflow_outputs": []\n }, \n- "3": {\n+ "4": {\n "annotation": "", \n "content_id": 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"input_connections": {\n "input1": {\n- "id": 5, \n+ "id": 6, \n "output_name": "out_file1"\n }, \n "input2": {\n- "id": 6, \n+ "id": 7, \n "output_name": "out_file1"\n }\n }, \n@@ -328,8 +360,8 @@\n }\n ], \n "position": {\n- "left": 1123.952163696289, \n- "top": 363.4558563232422\n+ "left": 1123.9375, \n+ "top": 363.453125\n }, \n "post_job_actions": {\n "HideDatasetActionout_file1": {\n@@ -346,13 +378,60 @@\n "uuid": "7c71fbae-828d-4c99-8f7b-fe1a90b27626", \n "workflow_outputs": []\n }, \n- "8": {\n+ "9": {\n+ "annotation": "", \n+ "content_id": "cat1", \n+ "id": 9, \n+ "input_connections": {\n+ "input1": {\n+ "id": 8, \n+ "output_name": "out_file1"\n+ }, \n+ "queries_0|input2": {\n+ "id": 2, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Concatenate datasets", \n+ "name": "input1"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Concatenate datasets", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 1130.5, \n+ "top": 686\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionout_file1": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "cat1", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"queries\\": \\"[{\\\\\\"input2\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"__index__\\\\\\": 0}]\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "uuid": "8a1e29ca-8dec-4143-9db1-f38f820b0e9a", \n+ "workflow_outputs": []\n+ }, \n+ "10": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", \n- "id": 8, \n+ "id": 10, \n "input_connections": {\n "identifiers": {\n- "id": 7, \n+ "id": 9, \n "output_name": "out_file1"\n }, \n "input": {\n@@ -379,8 +458,8 @@\n }\n ], \n "position": {\n- "left": 1129.9264068603516, \n- "top": 544.4669036865234\n+ "left": 1392.921875, \n+ "top": 550.453125\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -404,5 +483,5 @@\n ]\n }\n }, \n- "uuid": "23e0aa20-d91a-429e-817c-654a67b0a171"\n-}\n\\ No newline at end of file\n+ "uuid": "cf6b9210-2ed8-46b1-920e-ac6303ed44d5"\n+}\n' |
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| diff -r b92f5ab6d127 -r 267a94f068d7 finding_orphan_genes.png |
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| Binary file finding_orphan_genes.png has changed |
