Mercurial > repos > eschen42 > mqppep_anova
diff workflow/ppenrich_suite_wf.ga @ 7:d728198f1ba5 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
| author | eschen42 |
|---|---|
| date | Tue, 15 Mar 2022 00:35:16 +0000 |
| parents | c1403d18c189 |
| children |
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--- a/workflow/ppenrich_suite_wf.ga Fri Mar 11 20:04:05 2022 +0000 +++ b/workflow/ppenrich_suite_wf.ga Tue Mar 15 00:35:16 2022 +0000 @@ -28,20 +28,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 257.06666564941406, - "height": 81.39999389648438, - "left": 339.95001220703125, - "right": 539.9500122070312, - "top": 175.6666717529297, + "bottom": -36.30000305175781, + "height": 82.19999694824219, + "left": 150, + "right": 350, + "top": -118.5, "width": 200, - "x": 339.95001220703125, - "y": 175.6666717529297 + "x": 150, + "y": -118.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "002d55e6-29a5-426d-9248-70ec33424b15", + "uuid": "f4273d40-f2b8-4ad0-8bcc-91e72bd25fe1", "workflow_outputs": [] }, "1": { @@ -60,20 +60,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 411.4666748046875, - "height": 101.79998779296875, - "left": 379.95001220703125, - "right": 579.9500122070312, - "top": 309.66668701171875, + "bottom": 278.1000061035156, + "height": 102.60000610351562, + "left": 376, + "right": 576, + "top": 175.5, "width": 200, - "x": 379.95001220703125, - "y": 309.66668701171875 + "x": 376, + "y": 175.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}", "tool_version": null, "type": "data_input", - "uuid": "8f079dcc-1843-47cd-b4dc-1830e4466430", + "uuid": "cb31b0ac-cacc-42ee-bd42-f42d0bdae128", "workflow_outputs": [] }, "2": { @@ -92,20 +92,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 573.4666748046875, - "height": 101.79998779296875, - "left": 418.95001220703125, - "right": 618.9500122070312, - "top": 471.66668701171875, + "bottom": 423.1000061035156, + "height": 102.60000610351562, + "left": 387, + "right": 587, + "top": 320.5, "width": 200, - "x": 418.95001220703125, - "y": 471.66668701171875 + "x": 387, + "y": 320.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "dc894a94-97a3-40ff-811e-01b30d498478", + "uuid": "e6ec01b8-ff1a-4c90-a064-b40c5cad75bb", "workflow_outputs": [] }, "3": { @@ -124,20 +124,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 726.0666809082031, - "height": 81.39999389648438, - "left": 459.95001220703125, - "right": 659.9500122070312, - "top": 644.6666870117188, + "bottom": 546.6999969482422, + "height": 82.19999694824219, + "left": 399, + "right": 599, + "top": 464.5, "width": 200, - "x": 459.95001220703125, - "y": 644.6666870117188 + "x": 399, + "y": 464.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "6fc936ad-0b52-484f-a051-73c1776fdeb0", + "uuid": "2c59056a-c1b4-4a20-a194-991d56c8b6c2", "workflow_outputs": [] }, "4": { @@ -156,20 +156,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 894.4666748046875, - "height": 101.79998779296875, - "left": 503.95001220703125, - "right": 703.9500122070312, - "top": 792.6666870117188, + "bottom": 696.1000061035156, + "height": 102.60000610351562, + "left": 420, + "right": 620, + "top": 593.5, "width": 200, - "x": 503.95001220703125, - "y": 792.6666870117188 + "x": 420, + "y": 593.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "22b77482-2339-4b45-8fc6-d39f7175131b", + "uuid": "987a5891-15f1-4f70-89a8-386447f0bf24", "workflow_outputs": [] }, "5": { @@ -188,20 +188,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 1041.0666809082031, - "height": 81.39999389648438, - "left": 535.9500122070312, - "right": 735.9500122070312, - "top": 959.6666870117188, + "bottom": 820.6999969482422, + "height": 82.19999694824219, + "left": 436, + "right": 636, + "top": 738.5, "width": 200, - "x": 535.9500122070312, - "y": 959.6666870117188 + "x": 436, + "y": 738.5 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "3d97a902-1408-403c-b82e-ddb6ca6a7d47", + "uuid": "964d8d21-b063-411a-aee8-372a0d0dfba3", "workflow_outputs": [] }, "6": { @@ -220,20 +220,20 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 1210.5666198730469, - "height": 81.39999389648438, - "left": 562.9500122070312, - "right": 762.9500122070312, - "top": 1129.1666259765625, + "bottom": 1071.1999969482422, + "height": 82.19999694824219, + "left": 418, + "right": 618, + "top": 989, "width": 200, - "x": 562.9500122070312, - "y": 1129.1666259765625 + "x": 418, + "y": 989 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", "tool_version": null, "type": "data_input", - "uuid": "7b5eab97-7dad-4b0e-81eb-22aac39dd5b6", + "uuid": "42577db7-d5e5-4f39-b3ad-d0648abb9df3", "workflow_outputs": [] }, "7": { @@ -267,7 +267,32 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "networkin" + }, + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "p_sty_motifs" + }, + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "phosphoSites" + }, + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "protein_fasta" + }, + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "psp_kinase_substrate" + }, + { + "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", + "name": "psp_regulatory_sites" + } + ], "label": null, "name": "MaxQuant Phosphopeptide Preprocessing", "outputs": [ @@ -325,14 +350,14 @@ } ], "position": { - "bottom": 1186.6000366210938, - "height": 812.933349609375, - "left": 945.4500122070312, - "right": 1145.4500122070312, - "top": 373.66668701171875, + "bottom": 964.0999755859375, + "height": 793.5999755859375, + "left": 826.5, + "right": 1026.5, + "top": 170.5, "width": 200, - "x": 945.4500122070312, - "y": 373.66668701171875 + "x": 826.5, + "y": 170.5 }, "post_job_actions": { "RenameDatasetActionenrichGraph": { @@ -428,75 +453,75 @@ } }, "tool_id": "mqppep_preproc", - "tool_state": "{\"collapseFunc\": \"sum\", \"enriched\": \"ST\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"phospho_type\": \"sty\", \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0+galaxy0", + "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"RuntimeValue\"}, \"p_sty_motifs\": {\"__class__\": \"RuntimeValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"RuntimeValue\"}, \"protein_fasta\": {\"__class__\": \"RuntimeValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"RuntimeValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"RuntimeValue\"}, \"pst_not_py\": \"true\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": null, "type": "tool", - "uuid": "235b1a2e-ccc0-4c91-bb91-bbf4d272c870", + "uuid": "886043ce-8d9b-474e-b970-4fe9ee6a74fa", "workflow_outputs": [ { "label": "ppep_intensities", "output_name": "phosphoPepIntensities", - "uuid": "92fd4e27-5d4b-4e9f-b3ad-6bdad53bb93d" + "uuid": "e19a64d1-edee-4119-a72e-456af7a6c056" }, { "label": "enrichGraph_pdf", "output_name": "enrichGraph", - "uuid": "4c1d5590-f8ba-421c-858c-4c026691b52e" + "uuid": "7e9936d9-9617-4df4-9133-7a04f8d05d26" }, { "label": "locProbCutoffGraph_pdf", "output_name": "locProbCutoffGraph", - "uuid": "66a79534-6372-4937-bcf2-8644be985eea" + "uuid": "5656cba7-25e2-4362-ae92-1ddac67dee07" }, { "label": "enrichGraph_svg", "output_name": "enrichGraph_svg", - "uuid": "5e713d9c-1868-423b-be9a-25c0486e1472" + "uuid": "ca13a22e-a41b-481c-ab87-1f97bbf768e9" }, { "label": "locProbCutoffGraph_svg", "output_name": "locProbCutoffGraph_svg", - "uuid": "4621ea21-ae90-4547-a68f-30dfc7857368" + "uuid": "fc7a11f5-30d8-4409-878a-d3b70366711c" }, { "label": "filteredData", "output_name": "filteredData_tabular", - "uuid": "bb26d0fb-6f19-43c7-80ef-1cf81aa09ee8" + "uuid": "aab49fc5-a3cf-4479-ac23-8e9272dadf28" }, { "label": "quantData", "output_name": "quantData_tabular", - "uuid": "20efe04f-2700-4af0-92c6-0830a42d8e75" + "uuid": "23940202-403e-4256-916b-92539db07cdb" }, { "label": "ppep_map", "output_name": "mapped_phophopeptides", - "uuid": "037e2b97-8fc8-436d-bcc3-af5ee685b752" + "uuid": "08ad13d4-c103-4f18-92cc-2c3b58565981" }, { "label": "melted_phosphopeptide_map", "output_name": "melted_phophopeptide_map", - "uuid": "c3e5de84-2659-45eb-81a6-edef6037d8aa" + "uuid": "77cecaeb-8f7c-482e-b78a-e4809b194eb7" }, { "label": "ppep_mapping_sqlite", "output_name": "mqppep_output_sqlite", - "uuid": "a1a4f827-1f1f-4175-ae51-c238f9e1f248" + "uuid": "8e53e05a-a47c-4b97-87e4-ebab133ccaea" }, { "label": "preproc_tab", "output_name": "preproc_tab", - "uuid": "b22b4b56-9395-4f6d-945e-0089e8897069" + "uuid": "530a8140-9eba-4c87-a76b-4922febc12e7" }, { "label": "preproc_csv", "output_name": "preproc_csv", - "uuid": "54be90f9-1158-4686-af42-43d021088300" + "uuid": "c5f22f05-0bf7-48cf-adc0-c2beffe33169" }, { "label": "preproc_sqlite", "output_name": "preproc_sqlite", - "uuid": "33663f9c-b718-4bdd-acc9-087c76bea678" + "uuid": "53424150-7673-40af-ad60-0b4035e0c302" } ] }, @@ -529,14 +554,14 @@ } ], "position": { - "bottom": 1488.0999603271484, - "height": 254.93333435058594, - "left": 1202.949951171875, - "right": 1402.949951171875, - "top": 1233.1666259765625, + "bottom": 1349, + "height": 256, + "left": 1058, + "right": 1258, + "top": 1093, "width": 200, - "x": 1202.949951171875, - "y": 1233.1666259765625 + "x": 1058, + "y": 1093 }, "post_job_actions": { "RenameDatasetActionimputed_data_file": { @@ -556,19 +581,19 @@ }, "tool_id": "mqppep_anova", "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"first_data_column\": \"Intensity\", \"imputation\": {\"imputation_method\": \"group-median\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"sample_grouping_regex\": \"(\\\\d+)\", \"sample_names_regex\": \"\\\\.(\\\\d+)[A-Z]$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0+galaxy0", + "tool_version": null, "type": "tool", - "uuid": "2257286b-6f9a-45c1-90a3-bf5b972959d5", + "uuid": "a3cb902d-8ef6-4f84-bed3-80b2b20d1916", "workflow_outputs": [ { "label": "intensities_group-mean-imputed_QN_LT", "output_name": "imputed_data_file", - "uuid": "8e7317c6-95e9-4454-b4d7-31b4de6167a8" + "uuid": "ef19dcd3-8f3e-4fc4-829e-dae6719ff1cc" }, { "label": "intensities_group-mean-imputed_report", "output_name": "report_file", - "uuid": "dfe9b34e-1f3e-4971-8382-41178104e253" + "uuid": "26bb93b0-bc11-4455-a280-241253b21981" } ] }, @@ -601,14 +626,14 @@ } ], "position": { - "bottom": 1325.0999603271484, - "height": 254.93333435058594, - "left": 1452.949951171875, - "right": 1652.949951171875, - "top": 1070.1666259765625, + "bottom": 1186, + "height": 256, + "left": 1308, + "right": 1508, + "top": 930, "width": 200, - "x": 1452.949951171875, - "y": 1070.1666259765625 + "x": 1308, + "y": 930 }, "post_job_actions": { "RenameDatasetActionimputed_data_file": { @@ -628,19 +653,19 @@ }, "tool_id": "mqppep_anova", "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"first_data_column\": \"Intensity\", \"imputation\": {\"imputation_method\": \"random\", \"__current_case__\": 3, \"meanPercentile\": \"1\", \"sdPercentile\": \"0.2\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"sample_grouping_regex\": \"(\\\\d+)\", \"sample_names_regex\": \"\\\\.(\\\\d+)[A-Z]$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0+galaxy0", + "tool_version": null, "type": "tool", - "uuid": "9516971c-8532-4797-8bf9-4655ff104dbd", + "uuid": "217d92af-f6d6-4fd3-a78a-090d8afd3ae0", "workflow_outputs": [ { "label": "intensities_randomly-imputed_QN_LT", "output_name": "imputed_data_file", - "uuid": "8ceda029-d5fd-4d75-a2b3-ac582bb137c3" + "uuid": "925d734f-f9d8-49e8-aebb-c8d7598d45b2" }, { "label": "intensities_randomly-imputed_report", "output_name": "report_file", - "uuid": "84bedf25-c15b-4cc7-97e0-92f746e89f9c" + "uuid": "4ab5f1b1-d04e-4634-8765-265122bc1064" } ] } @@ -648,6 +673,6 @@ "tags": [ "ppenrich" ], - "uuid": "ac7bf2d1-89fe-4bf6-920a-d5508842d3f9", - "version": 7 + "uuid": "c54c2b2e-8080-445c-bc3e-43950c89d4e4", + "version": 3 } \ No newline at end of file