From d7fa5bc623fe6a90a1da0dfbb3c187b7038934df Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 21 Oct 2022 10:15:10 +0200 Subject: [PATCH] hide the output of revertR2 --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 216 ++++++++---------- 1 file changed, 92 insertions(+), 124 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 686e9eded..40c074d68 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -29,8 +29,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, - "top": 198.9718598204774 + "left": 0, + "top": 198.9666748046875 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -55,21 +55,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 16.910206187855124, - "top": 271.88853474406454 + "left": 16.916671752929688, + "top": 271.8833312988281 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "0179b655-f7e2-4b8b-b8b1-f875d0d8039f", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d4a5d221-29f4-469d-ad39-63c56bab4e8c" - } - ] + "workflow_outputs": [] }, "2": { "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", @@ -87,21 +81,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 51.00111527876419, - "top": 361.904763556146 + "left": 51, + "top": 361.8999938964844 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "2cf82136-4f80-43f5-bf2d-fde510bf8a93", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "fd771191-a632-4627-ab8a-e61218e8bc6d" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "reference_genome", @@ -119,21 +107,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 89.06926737203224, - "top": 451.9210171389889 + "left": 89.06666564941406, + "top": 451.9166717529297 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "ff4a9932-6ed0-436f-a63c-d6fbe2a582a3", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "166cd0f5-a879-4612-8c29-75fb551fbc92" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", @@ -151,8 +133,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 131.76410229175121, - "top": 538.9069396179991 + "left": 131.76666259765625, + "top": 538.8999938964844 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -177,21 +159,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 183.8474025974026, - "top": 617.9383265507685 + "left": 183.85000610351562, + "top": 617.9333343505859 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "fd2c51fd-58b3-43b5-b8ce-a919f5325cb7", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "256611c9-4c6f-4e21-823c-f75989cc4421" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -209,8 +185,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 241.93721622615658, - "top": 692.8030484682553 + "left": 241.93333435058594, + "top": 692.8000030517578 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -252,8 +228,8 @@ } ], "position": { - "left": 286.0660305270901, - "top": 183.68505502676038 + "left": 286.066650390625, + "top": 183.683349609375 }, "post_job_actions": { "HideDatasetActionout_pairs": { @@ -301,8 +277,8 @@ } ], "position": { - "left": 940.6115048891536, - "top": 1100.0000099083045 + "left": 940.61669921875, + "top": 1100 }, "post_job_actions": { "HideDatasetActionout1": { @@ -345,8 +321,8 @@ } ], "position": { - "left": 539.0692376471185, - "top": 603.0844155844155 + "left": 539.066650390625, + "top": 603.0833282470703 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -389,8 +365,8 @@ } ], "position": { - "left": 1119.1016853629767, - "top": 675.0000049541522 + "left": 1119.0999755859375, + "top": 675 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -433,8 +409,8 @@ } ], "position": { - "left": 1144.1017249961951, - "top": 901.9210121848365 + "left": 1144.0999755859375, + "top": 901.9166870117188 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -477,8 +453,8 @@ } ], "position": { - "left": 984.6861207640015, - "top": 1283.0357241940187 + "left": 984.683349609375, + "top": 1283.0333251953125 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -541,8 +517,8 @@ } ], "position": { - "left": 573.0789977234679, - "top": 182.7651680289925 + "left": 573.0833129882812, + "top": 182.76666259765625 }, "post_job_actions": { "HideDatasetActionsplice_junctions": { @@ -566,17 +542,17 @@ { "label": "mapped-reads", "output_name": "mapped_reads", - "uuid": "49808224-b9b5-4ae0-9aab-8aa33202ed86" + "uuid": "9f1e63ab-5b1f-498d-bd4e-96c849442837" }, { "label": "output_log", "output_name": "output_log", - "uuid": "21df3931-dd5c-4391-9ed8-89f9da87af5a" + "uuid": "e33a3f72-9b45-4673-8461-9070c296111b" }, { "label": "reads_per_gene from STAR", "output_name": "reads_per_gene", - "uuid": "fe32ff38-6ecf-4121-9a68-5832f65f3c32" + "uuid": "6219c8ec-2a83-4902-a96f-241308316788" } ] }, @@ -617,8 +593,8 @@ } ], "position": { - "left": 843.7499999999998, - "top": 0.0 + "left": 843.75, + "top": 0 }, "post_job_actions": { "HideDatasetActionplots": { @@ -639,15 +615,15 @@ "type": "tool", "uuid": "a4e1b954-a475-4a3c-b84a-5dc44947e1c8", "workflow_outputs": [ - { - "label": "MultiQC on input dataset(s): Stats", - "output_name": "stats", - "uuid": "b03052c4-9a89-478d-bf50-246e4cdeb283" - }, { "label": "MultiQC webpage", "output_name": "html_report", - "uuid": "d6dee2dd-b224-4cc0-b094-eb97bfa50ba6" + "uuid": "b7d71c2a-1ad3-4a6a-b8f8-13347b19be1d" + }, + { + "label": "MultiQC on input dataset(s): Stats", + "output_name": "stats", + "uuid": "e9897bd6-7557-41b3-898b-5d6ce31af801" } ] }, @@ -676,8 +652,8 @@ } ], "position": { - "left": 804.3831168831168, - "top": 432.76516802899243 + "left": 804.38330078125, + "top": 432.76666259765625 }, "post_job_actions": { "RenameDatasetActionoutfile": { @@ -703,7 +679,7 @@ { "label": "HTS count like output", "output_name": "outfile", - "uuid": "34912c4a-4897-473a-8436-f969bec9d07f" + "uuid": "41e78153-6863-4b74-abee-4f0f8313c27f" } ] }, @@ -732,8 +708,8 @@ } ], "position": { - "left": 830.8441360275465, - "top": 605.0595370205965 + "left": 830.8499755859375, + "top": 605.0666656494141 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -781,8 +757,8 @@ } ], "position": { - "left": 1143.9664766385956, - "top": 239.3939526050122 + "left": 1143.9666748046875, + "top": 239.39999389648438 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -831,20 +807,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "input" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "reference_annotation" - } - ], + "inputs": [], "label": "Compute FPKM", "name": "Cufflinks", "outputs": [ @@ -870,8 +833,8 @@ } ], "position": { - "left": 1036.9859175248578, - "top": 1426.70455536285 + "left": 1036.9833984375, + "top": 1426.7000122070312 }, "post_job_actions": { "HideDatasetActionassembled_isoforms": { @@ -897,7 +860,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"RuntimeValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"RuntimeValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": \"true\", \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"RuntimeValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": \"true\", \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1.3", "type": "tool", "uuid": "a3371ab0-86dd-4302-bdbc-4e79421186d9", @@ -905,12 +868,12 @@ { "label": "genes_expression", "output_name": "genes_expression", - "uuid": "f9ca5874-f167-410f-bee1-d3d694d11b89" + "uuid": "72762de7-59db-4fa7-bfba-49bcd312e4c0" }, { "label": "transcripts_expression", "output_name": "transcripts_expression", - "uuid": "81f8292d-151b-448c-bb98-7b4c6fb8b6fd" + "uuid": "9b95e51f-e143-4f22-b069-db446565c685" } ] }, @@ -925,7 +888,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool revertR2orientationInBam", + "name": "input" + } + ], "label": null, "name": "revertR2orientationInBam", "outputs": [ @@ -935,10 +903,16 @@ } ], "position": { - "left": 984.4426737203225, - "top": 812.256503414798 + "left": 984.4500122070312, + "top": 812.25 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2", "tool_shed_repository": { "changeset_revision": "21ddefab2e4f", @@ -946,17 +920,11 @@ "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.2", "type": "tool", "uuid": "405ecc3a-86fc-4371-8857-5f5c13d35360", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9a47fad1-47f6-4354-8269-2dc4cc6b4e43" - } - ] + "workflow_outputs": [] }, "20": { "annotation": "", @@ -979,8 +947,8 @@ } ], "position": { - "left": 1342.3159710772625, - "top": 364.25867947665125 + "left": 1342.316650390625, + "top": 364.26666259765625 }, "post_job_actions": { "HideDatasetActionfloat_param": { @@ -1021,8 +989,8 @@ } ], "position": { - "left": 1374.5401555841618, - "top": 547.1049965202034 + "left": 1374.5333251953125, + "top": 547.1000061035156 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1073,8 +1041,8 @@ } ], "position": { - "left": 1388.0412114130984, - "top": 765.0162337662337 + "left": 1388.0333251953125, + "top": 765.0166625976562 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1125,8 +1093,8 @@ } ], "position": { - "left": 1395.0487607485286, - "top": 1018.7229800533937 + "left": 1395.050048828125, + "top": 1018.7166748046875 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1169,8 +1137,8 @@ } ], "position": { - "left": 1614.8809457754157, - "top": 604.1396252520672 + "left": 1614.88330078125, + "top": 604.1333312988281 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -1190,7 +1158,7 @@ { "label": "both strands coverage", "output_name": "out_file1", - "uuid": "983438e5-556c-464e-b5eb-7a13e3a60970" + "uuid": "2628ff9d-fafb-46c4-8d7a-5337cde22115" } ] }, @@ -1215,8 +1183,8 @@ } ], "position": { - "left": 1653.0843957678062, - "top": 781.8993655118074 + "left": 1653.0833740234375, + "top": 781.8999938964844 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -1236,7 +1204,7 @@ { "label": "positive strand coverage", "output_name": "out_file1", - "uuid": "ca81c4e5-2f8d-4753-80ca-a87814b01614" + "uuid": "9359582f-9bc7-4308-9a7f-72571dd43b9d" } ] }, @@ -1261,8 +1229,8 @@ } ], "position": { - "left": 1679.9783087396, - "top": 1000.8658124254894 + "left": 1679.9833984375, + "top": 1000.8666687011719 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -1282,7 +1250,7 @@ { "label": "negative strand coverage", "output_name": "out_file1", - "uuid": "d0c57c2c-2e61-4f7a-a4bc-c9234084d223" + "uuid": "1fbf821a-ff58-4c2a-b4be-386bf19b8bc8" } ] } @@ -1290,6 +1258,6 @@ "tags": [ "RNAseq" ], - "uuid": "176940ea-5051-47bd-ab5d-0b85f0b3f385", - "version": 3 + "uuid": "5b946edc-98aa-43d9-b416-978e6e8053f4", + "version": 1 } \ No newline at end of file