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+ "inputs": [ + { + "description": "runtime parameter for tool Plot actual vs predicted curves and residual plots", + "name": "infile_input" + }, + { + "description": "runtime parameter for tool Plot actual vs predicted curves and residual plots", + "name": "infile_output" + } + ], "label": null, "name": "Plot actual vs predicted curves and residual plots", "outputs": [ @@ -312,8 +458,14 @@ } ], "position": { - "left": 890, - "top": 10 + "bottom": 560.6817932128906, + "height": 367.7130432128906, + "left": 1272.9970703125, + "right": 1472.9970703125, + "top": 192.96875, + "width": 200, + "x": 1272.9970703125, + "y": 192.96875 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1", @@ -323,11 +475,27 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"tsv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile_input\": null, \"infile_output\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"infile_input\": {\"__class__\": \"RuntimeValue\"}, \"infile_output\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1", "type": "tool", "uuid": "4ba08ee0-dbdd-4b6a-8fc2-5eea1af0e567", - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output_actual_vs_pred", + "uuid": "74eae0e4-6b80-4091-b46a-16c58d2ce36b" + }, + { + "label": null, + "output_name": "output_scatter_plot", + "uuid": "5f42df99-c504-47b0-bb0a-9b6033141413" + }, + { + "label": null, + "output_name": "output_residual_plot", + "uuid": "2c6b76a6-0869-4ab6-84bc-11d555ab1b2f" + } + ] } }, "tags": [ @@ -335,6 +503,6 @@ "ml", "fnn" ], - "uuid": "c702d3a4-3998-4b48-9822-7c4eff14b052", - "version": 0 + "uuid": "85038aae-2c0f-42c6-9be7-686906fd1b00", + "version": 1 } \ No newline at end of file diff --git a/GTN/RNN_Intro_To_RNN.ga b/GTN/RNN_Intro_To_RNN.ga index e699ef6..2fd257f 100644 --- a/GTN/RNN_Intro_To_RNN.ga +++ b/GTN/RNN_Intro_To_RNN.ga @@ -17,14 +17,20 @@ } ], "label": "X_test", - "name": "X_test", + "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 10 + "bottom": 342.6988639831543, + "height": 61.73295211791992, + "left": 680.9801025390625, + "right": 880.9801025390625, + "top": 280.9659118652344, + "width": 200, + "x": 680.9801025390625, + "y": 280.9659118652344 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "a5e70504-f58c-4e47-898e-e19862e263c8", @@ -43,14 +49,20 @@ } ], "label": "X_train", - "name": "X_train", + "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 130 + "bottom": 462.72724533081055, + "height": 61.73295211791992, + "left": 680.9801025390625, + "right": 880.9801025390625, + "top": 400.9942932128906, + "width": 200, + "x": 680.9801025390625, + "y": 400.9942932128906 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "8628fa07-9b42-43c3-9dfd-bb2a0a4b37e6", @@ -69,14 +81,20 @@ } ], "label": "y_test", - "name": "y_test", + "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 250 + "bottom": 582.7130546569824, + "height": 61.73295211791992, + "left": 680.9801025390625, + "right": 880.9801025390625, + "top": 520.9801025390625, + "width": 200, + "x": 680.9801025390625, + "y": 520.9801025390625 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "b832ca33-c953-482f-a600-45bdbdfdbf61", @@ -95,14 +113,20 @@ } ], "label": "y_train", - "name": "y_train", + "name": "Input dataset", "outputs": [], "position": { - "left": 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"toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"dataset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", + "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0", "type": "tool", "uuid": "465a0ecf-4f47-4679-ad02-c06eb48449fc", "workflow_outputs": [ { "label": null, - "output_name": "stats", - "uuid": "9b126d55-16aa-4a62-9c26-5e46042fcc93" + "output_name": "stats_output", + "uuid": "ae93f473-d571-439c-8fa6-3927026fdb49" } ] }, @@ -725,14 +628,8 @@ } ], "position": { - "bottom": 886.9375305175781, - "height": 243.33334350585938, - "left": 848.75, - "right": 1048.75, - "top": 643.6041870117188, - "width": 200, - "x": 848.75, - "y": 643.6041870117188 + "left": 1195.359375, + "top": 628.0546875 }, "post_job_actions": { "RenameDatasetActionbam_output": { @@ -745,7 +642,7 @@ }, 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"da1cc1bc-e00c-4f65-afbc-1a118b23274a" }, { "label": null, - "output_name": "out_tsv", - "uuid": "db4d1a46-81e5-42a8-bd72-bfe2a19d1af1" + "output_name": "out_sqn", + "uuid": "a5a04271-fc67-4ce3-95dc-9f01ee77775c" }, { "label": null, - "output_name": "out_txt", - "uuid": "90d1eb7c-26f0-452e-891d-4965a1e77114" + "output_name": "out_log", + "uuid": "ca98afab-a3d2-4beb-b3f0-de7f38bf5c6b" }, { "label": null, "output_name": "out_gff", - "uuid": "df5aa92b-edd1-4bb5-8acd-abfff59a9735" + "uuid": "bae78be6-7c70-42bf-95c1-cae45c51871d" }, { "label": null, - "output_name": "out_log", - "uuid": "8112c5ed-aefa-4d3d-b66d-69c00c4f3e64" + "output_name": "out_gbk", + "uuid": "9a2a7aab-fde6-4a9c-b098-17b958ff2f20" } ] }, @@ -997,12 +882,7 @@ "output_name": "bam_output" } }, - "inputs": [ - { - "description": "runtime parameter for tool JBrowse", - "name": "reference_genome" - } - ], + "inputs": [], "label": null, "name": "JBrowse", "outputs": [ @@ -1012,14 +892,8 @@ } ], "position": { - "bottom": 867.6875305175781, - "height": 293.3333435058594, - "left": 1122.5, - "right": 1322.5, - "top": 574.3541870117188, - "width": 200, - "x": 1122.5, - "y": 574.3541870117188 + "left": 1469.125, + "top": 558.828125 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -1037,7 +911,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": 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{\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.16.9+galaxy0", "type": "tool", "uuid": "9ae0aa01-72e9-4481-b992-248f3ec20a07", @@ -1045,7 +919,7 @@ { "label": null, "output_name": "output", - "uuid": "1ba60bd6-3fd8-4813-84d1-b61312e6610f" + "uuid": "b5c7a4ed-bb41-4486-b01f-270071e23e52" } ] }, @@ -1064,12 +938,7 @@ "output_name": "out_gff" } }, - "inputs": [ - { - "description": "runtime parameter for tool JBrowse", - "name": "reference_genome" - } - ], + "inputs": [], "label": null, "name": "JBrowse", "outputs": [ @@ -1079,14 +948,8 @@ } ], "position": { - "bottom": 463.18751525878906, - "height": 223.33334350585938, - "left": 1634.75, - "right": 1834.75, - "top": 239.8541717529297, - "width": 200, - "x": 1634.75, - "y": 239.8541717529297 + "left": 1981.40625, + "top": 224.328125 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -1104,7 +967,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, 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\"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.16.9+galaxy0", "type": "tool", "uuid": "7e5c8b63-2538-4898-9644-71453e17c0ba", @@ -1112,7 +975,7 @@ { "label": null, "output_name": "output", - "uuid": "4d1ebaa1-b8f0-441d-bb60-ef946ca6d2e8" + "uuid": "5ad68433-82c3-47aa-b3e4-ef1b07ed790e" } ] } @@ -1120,6 +983,6 @@ "tags": [ "assembly" ], - "uuid": "b9e0e8b2-9895-4d74-99e4-dca6ac4dd9bf", - "version": 19 + "uuid": "e86f3679-9409-4b7a-88fc-66cf83c860e5", + "version": 4 } \ No newline at end of file diff --git a/GTN/circos_main_workflow.ga b/GTN/circos_main_workflow.ga index 83b3669..bf7b65f 100644 --- a/GTN/circos_main_workflow.ga +++ b/GTN/circos_main_workflow.ga @@ -1,8 +1,21 @@ { "a_galaxy_workflow": "true", "annotation": "Visualisation with Circos", + "creator": [ + { + "class": "Person", + "identifier": "0000-0001-9760-8992", + "name": "Helena Rasche" + }, + { + "class": "Person", + "identifier": "0000-0003-3803-468X", + "name": "Saskia Hiltemann" + } + ], "format-version": "0.1", - "name": "Workflow Constructed From History 'Workflow Constructed From History 'Workflow Constructed From History 'Circos Tutorial'''", + "license": "AGPL-3.0-or-later", + "name": 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image\")\n```\n\n## Quast results\n\n\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s): tabular report\")\n```\n\n\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Polished assembly" + } + ], + "label": "Polished assembly", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 331.765625, + "height": 82.171875, + "left": 447.734375, + "right": 647.734375, + "top": 249.59375, + "width": 200, + "x": 447.734375, + "y": 249.59375 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "2ed19084-9eaf-4efb-acdc-b81536e7c024", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome" + } + ], + "label": "Reference 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Analysis with mothur (short)", "format-version": "0.1", + "license": "MIT", + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0003-3803-468X", + "name": "Saskia Hiltemann" + } + ], "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]", "steps": { "0": { diff --git a/GTN/mothur-miseq-sop-short_workflow2_data_cleaning.ga b/GTN/mothur-miseq-sop-short_workflow2_data_cleaning.ga index aa7fd9b..9af446b 100644 --- a/GTN/mothur-miseq-sop-short_workflow2_data_cleaning.ga +++ b/GTN/mothur-miseq-sop-short_workflow2_data_cleaning.ga @@ -1,7 +1,15 @@ { "a_galaxy_workflow": "true", "annotation": "16S Microbial Analysis with mothur (short)", + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0003-3803-468X", + "name": "Saskia Hiltemann" + } + ], "format-version": "0.1", + "license": "MIT", "name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]", 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"post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0", @@ -682,10 +646,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.39.5.0", "type": "tool", "uuid": "9a018d5e-23f7-46a7-ac83-a57bc2ddd9ac", + "when": null, "workflow_outputs": [ { "label": null, @@ -698,6 +663,6 @@ "tags": [ "metagenomics" ], - "uuid": "754f276d-2021-422b-840c-f84be221315c", - "version": 2 + "uuid": "aeb17171-67a7-4ef7-b9ce-849fc81e3de6", + "version": 1 } \ No newline at end of file diff --git a/GTN/mothur-miseq-sop-short_workflow3_classification.ga b/GTN/mothur-miseq-sop-short_workflow3_classification.ga index ff1d28d..af943e4 100644 --- a/GTN/mothur-miseq-sop-short_workflow3_classification.ga +++ b/GTN/mothur-miseq-sop-short_workflow3_classification.ga @@ -1,7 +1,15 @@ { "a_galaxy_workflow": "true", "annotation": "16S Microbial Analysis with mothur (short)", + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0003-3803-468X", + "name": "Saskia Hiltemann" + } + ], "format-version": "0.1", + "license": "MIT", "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]", "steps": { "0": { @@ -20,27 +28,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 305.6999969482422, - "height": 82.19999694824219, - "left": 336, - "right": 536, - "top": 223.5, - "width": 200, - "x": 336, - "y": 223.5 + "left": 27, + "top": 123.5 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "817445c0-3b76-4949-bbed-34c88e2a0c59", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c3430894-50f2-42f6-886e-6972d8f97571" - } - ] + "when": null, + "workflow_outputs": [] }, "1": { "annotation": "", @@ -58,27 +55,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 466.3000030517578, - "height": 61.80000305175781, - "left": 309, - "right": 509, - "top": 404.5, - "width": 200, - "x": 309, - "y": 404.5 + "left": 0, + "top": 304.5 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "7b43d972-886f-4aae-ab0e-2fd188655cbd", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "af430c89-0e26-4129-a517-c2cc55235306" - } - ] + "when": null, + "workflow_outputs": [] }, "2": { "annotation": "", @@ -96,27 +82,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 697.6999969482422, - "height": 82.19999694824219, - "left": 313, - "right": 513, - "top": 615.5, - "width": 200, - "x": 313, - "y": 615.5 + "left": 4, + "top": 515.5 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f2ee2034-e7ce-43b0-82c9-905c2dd0745c", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "754b3f51-c344-4d70-a3d5-1a19ddca10aa" - } - ] + "when": null, + "workflow_outputs": [] }, "3": { "annotation": "", @@ -134,27 +109,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 876.6999969482422, - "height": 82.19999694824219, - "left": 339, - "right": 539, - "top": 794.5, - "width": 200, - "x": 339, - "y": 794.5 + "left": 30, + "top": 694.5 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f1a29c9e-a70e-4d8c-b7b4-1236da5245a1", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ecb05fa5-479b-4b41-9379-c653d314ef5d" - } - ] + "when": null, + "workflow_outputs": [] }, "4": { "annotation": "", @@ -197,14 +161,8 @@ } ], "position": { - "bottom": 559.2000122070312, - "height": 459.20001220703125, - "left": 847, - "right": 1047, - "top": 100, - "width": 200, - "x": 847, - "y": 100 + "left": 538, + "top": 0 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0", @@ -214,10 +172,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"alignment\": {\"source\": \"hist\", \"__current_case__\": 1, \"template\": null}, \"chromInfo\": 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"name": "count" + }, + { + "description": "runtime parameter for tool Summary.seqs", + "name": "fasta" + }, + { + "description": "runtime parameter for tool Summary.seqs", + "name": "name" + } + ], + "label": null, + "name": "Summary.seqs", + "outputs": [ + { + "name": "logfile", + "type": "txt" + }, + { + "name": "out_summary", + "type": "mothur.summary" + } + ], + "position": { + "left": 1128.25, + "top": 788.0624885559082 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0", + "tool_shed_repository": { + "changeset_revision": "609770e516fa", + "name": "mothur_summary_seqs", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.39.5.0", + "type": "tool", + "uuid": "c399d175-5b43-45b1-9916-f2f11f1cad25", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "logfile", + "uuid": "2ba6776c-d197-4804-9654-039b997986ce" + }, + { + "label": null, + "output_name": "out_summary", + "uuid": "b5e93d2a-6ff7-48bb-aa4e-5a58683910c8" } ] } @@ -298,6 +341,6 @@ "tags": [ "metagenomics" ], - "uuid": "cf10a048-802f-4eed-926e-87e205d92722", + "uuid": "2ea59846-fab6-4d97-b224-e9061014f1b8", "version": 1 } \ No newline at end of file diff --git a/GTN/mothur-miseq-sop-short_workflow4_mock_otu_clustering.ga b/GTN/mothur-miseq-sop-short_workflow4_mock_otu_clustering.ga index d0b52a2..8542486 100644 --- a/GTN/mothur-miseq-sop-short_workflow4_mock_otu_clustering.ga +++ b/GTN/mothur-miseq-sop-short_workflow4_mock_otu_clustering.ga @@ -1,7 +1,15 @@ { "a_galaxy_workflow": "true", "annotation": "16S Microbial Analysis with mothur (short)", + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0003-3803-468X", + "name": "Saskia Hiltemann" + } + ], "format-version": "0.1", + "license": "MIT", "name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]", "steps": { "0": { @@ -20,27 +28,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 214.1999969482422, - "height": 82.19999694824219, - "left": 87, - "right": 287, - "top": 132, - "width": 200, - "x": 87, - "y": 132 + "left": 0, + "top": 11 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "3c149509-370a-47f2-9f6d-a0fadcd7c1b6", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f3b1e914-d44a-4f4e-8206-84c71d8d3111" - } - ] + "when": null, + "workflow_outputs": [] }, "1": { "annotation": "", @@ -58,27 +55,16 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 462.1999969482422, - "height": 82.19999694824219, - "left": 94, - "right": 294, - "top": 380, - "width": 200, - "x": 94, - "y": 380 + "left": 7, + "top": 259 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "c020d492-fb13-43c7-85e3-faa820866965", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d84305b0-9a9e-4f12-ab31-9707b57bb31a" - } - ] + "when": null, + "workflow_outputs": [] }, "2": { "annotation": "", @@ -101,14 +87,8 @@ } ], "position": { - "bottom": 614.8000030517578, - "height": 174.8000030517578, - "left": 363, - "right": 563, - "top": 440, - "width": 200, - "x": 363, - "y": 440 + "left": 276, + "top": 319 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0", @@ -118,10 +98,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": 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+ "left": 570, + "top": 189 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0", @@ -180,10 +155,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"cutoff\": \"0.0\", \"matrix\": {\"format\": \"column\", \"__current_case__\": 0, \"dist\": {\"__class__\": \"ConnectedValue\"}, \"name\": null}, \"precision\": \"100\", \"savelog\": \"false\", \"select_method\": {\"method\": \"opti\", \"__current_case__\": 5, \"metric\": \"mcc\", \"initialize\": \"singleton\", \"delta\": \"0.0001\", \"iters\": \"100\"}, \"sim\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"cutoff\": \"0.0\", \"matrix\": {\"format\": \"column\", 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