From 198f6b6a9df7994dbb9622a1a1ceab99d616ebfe Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Mon, 11 Dec 2017 14:07:59 +0100 Subject: [PATCH 01/11] Subwf Succesfully invokation --- .../with-subworkflow/Galaxy-Workflow-MultiRoundClustering.ga | 1 + .../with-subworkflow/Galaxy-Workflow-iterative_clustering.ga | 1 + .../with-subworkflow/Galaxy-Workflow-iterative_clustering_r1.ga | 1 + 3 files changed, 3 insertions(+) create mode 100644 workflows/with-subworkflow/Galaxy-Workflow-MultiRoundClustering.ga create mode 100644 workflows/with-subworkflow/Galaxy-Workflow-iterative_clustering.ga create mode 100644 workflows/with-subworkflow/Galaxy-Workflow-iterative_clustering_r1.ga diff --git a/workflows/with-subworkflow/Galaxy-Workflow-MultiRoundClustering.ga b/workflows/with-subworkflow/Galaxy-Workflow-MultiRoundClustering.ga new file mode 100644 index 0000000..f3d842f --- /dev/null +++ b/workflows/with-subworkflow/Galaxy-Workflow-MultiRoundClustering.ga @@ -0,0 +1 @@ +{"uuid": 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b/workflows/GraphClust-MotifFinder.ga @@ -2,11 +2,12 @@ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", - "name": "MotifFinder (imported from API)", + "name": "MotifFinder (imported from API) (imported from API) (imported from API)", "steps": { "0": { "annotation": "", "content_id": null, + "errors": null, "id": 0, "input_connections": {}, "inputs": [ @@ -19,10 +20,9 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 206, - "top": 249 + "left": 187.984375, + "top": 199.96875 }, - "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, @@ -38,7 +38,8 @@ }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.2", + "errors": null, "id": 1, "input_connections": { "fastaFile": { @@ -50,6 +51,10 @@ { "description": "runtime parameter for tool Preprocessing", "name": "fastaFile" + }, + { + "description": "runtime parameter for tool Preprocessing", + "name": "SHAPEdata" } ], "label": null, @@ -74,11 +79,15 @@ { "name": "FASTA", "type": "zip" + }, + { + "name": "shape_data_split", + "type": "txt" } ], "position": { - "left": 381.984375, - "top": 301.984375 + "left": 299.96875, + "top": 278.984375 }, "post_job_actions": { "HideDatasetActionFASTA": { @@ -107,23 +116,29 @@ "output_name": "data.names" } }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.2", "tool_shed_repository": { - "changeset_revision": "8e6617badf0e", + "changeset_revision": "16bcaef3dc1e", "name": "graphclust_preprocessing", "owner": "rnateam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"fastaFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"in_winShift\": \"\\\"30\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_seq_length\": \"\\\"5\\\"\", \"max_length\": \"\\\"50\\\"\"}", - "tool_version": "0.1", + "tool_state": "{\"fastaFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"in_winShift\": \"\\\"30\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_seq_length\": \"\\\"5\\\"\", \"max_length\": \"\\\"50\\\"\", \"SHAPEdata\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.2", "type": "tool", "uuid": "0e367ec4-acb3-4f38-93ba-4c900aee99d0", - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "shape_data_split", + "uuid": "0ea69c85-a979-443c-8c7e-4d629de91dda" + } + ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_fasta_to_gspan/gspan/0.1", + "errors": null, "id": 2, "input_connections": { "dataFasta": { @@ -141,25 +156,24 @@ "name": "fasta_to_gspan", "outputs": [ { - "name": "gspan.zip", - "type": "searchgui_archive" + "name": "gspan_compressed", + "type": "input" } ], "position": { - "left": 579.96875, - "top": 166 + "left": 511.984375, + "top": 113.484375 }, "post_job_actions": { - "HideDatasetActiongspan.zip": { + "HideDatasetActiongspan_compressed": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "gspan.zip" + "output_name": "gspan_compressed" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_fasta_to_gspan/gspan/0.1", "tool_shed_repository": { - "changeset_revision": "6942ec989fed", + "changeset_revision": "fcb1bb6dc0f9", "name": "graphclust_fasta_to_gspan", "owner": "rnateam", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -167,12 +181,13 @@ "tool_state": "{\"__page__\": 0, \"group\": \"\\\"10000\\\"\", \"shift\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"M\": \"\\\"5\\\"\", \"dataFasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"i_crop_unpaired_ends\": \"\\\"false\\\"\", \"i_abstr\": \"\\\"false\\\"\", \"wins\": 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NSPDK_candidateClusters", - "name": "data_svector" + "name": "data_names" } ], "label": null, @@ -288,8 +303,8 @@ } ], "position": { - "left": 610.984375, - "top": 451.984375 + "left": 769.96875, + "top": 451.96875 }, "post_job_actions": { "HideDatasetActionblack_list": { @@ -323,15 +338,14 @@ "output_name": "fast_cluster_sim_m" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2", "tool_shed_repository": { - "changeset_revision": "d10410cfd17a", + "changeset_revision": "2aaf391798a3", "name": "graphclust_nspdk", "owner": "rnateam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"knn\": \"\\\"20\\\"\", \"max_dist_relations\": \"\\\"3\\\"\", \"nhf\": \"\\\"500\\\"\", \"noCache\": \"\\\"true\\\"\", \"__page__\": 0, \"usn\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"oc\": \"\\\"true\\\"\", \"iteration_num\": \"{\\\"iteration_num_selector\\\": \\\"false\\\", \\\"CI\\\": \\\"1\\\", 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+463,7 @@ "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.1.0", + "errors": null, "id": 6, "input_connections": { "center_fa_file": { @@ -495,8 +510,8 @@ } ], "position": { - "left": 1093.5, - "top": 389 + "left": 1251.484375, + "top": 385.984375 }, "post_job_actions": { "HideDatasetActionmodel_tree_stk": { @@ -505,15 +520,14 @@ "output_name": "model_tree_stk" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.1.0", "tool_shed_repository": { - "changeset_revision": "606440a3852d", + "changeset_revision": "98e9bc1fb249", "name": "graphclust_mlocarna", "owner": "rnateam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"center_fa_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"tree_matrix\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"allow_overlap\": \"\\\"false\\\"\", 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\"gap_threshold_opts\": \"{\\\"gap_threshold_opts_selector\\\": \\\"--g\\\", \\\"__current_case__\\\": 0, \\\"gap\\\": \\\"0.5\\\"}\"}", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"gap_threshold_opts\": \"{\\\"gap_threshold_opts_selector\\\": \\\"--g\\\", \\\"__current_case__\\\": 0, \\\"gap\\\": \\\"0.5\\\"}\", \"model_tree_stk\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"cmfinder_fa\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.1.0", "type": "tool", "uuid": "03a78407-d5d6-4c78-ba39-170b52702be2", @@ -579,6 +593,7 @@ "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.0.2", + "errors": null, "id": 8, "input_connections": { "alignment_infile": { @@ -609,8 +624,8 @@ } ], "position": { - "left": 1290, - "top": 666.984375 + "left": 1456.984375, + "top": 662.96875 }, "post_job_actions": { "HideDatasetActioncmfile_outfile": { @@ -629,7 +644,6 @@ "output_name": 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1 deletion(-) diff --git a/welcome.html b/welcome.html index eb03ea1..cf71b2f 100644 --- a/welcome.html +++ b/welcome.html @@ -14,7 +14,7 @@

Hello, your Galaxy Docker GraphClust container is running!<

How to start:

A quick and easy way to get familiar with Galaxy and Galaxy-GraphClust would be to visit the interactive tours provided under Help → Interactive Tours. Or simply click on the Guided Tour button below to start a tour.
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"inputs": [{"name": "model_tree_files", "description": "runtime parameter for tool cluster_collection_report"}, {"name": "FASTA", "description": "runtime parameter for tool cluster_collection_report"}, {"name": "cmsearch_results", "description": "runtime parameter for tool cluster_collection_report"}, {"name": "cdhit", "description": "runtime parameter for tool cluster_collection_report"}], "position": {"top": 1143.390625, "left": 3207.859375}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.3", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"} \ No newline at end of file diff --git a/workflows/GraphClust_2r_brnashapes.ga b/workflows/extra-workflows/GraphClust_2r_brnashapes.ga similarity index 100% rename from workflows/GraphClust_2r_brnashapes.ga rename to workflows/extra-workflows/GraphClust_2r_brnashapes.ga diff --git a/workflows/GraphClust_2r_vrnafold_SHAPE.ga b/workflows/extra-workflows/GraphClust_2r_vrnafold_SHAPE.ga similarity index 100% rename from workflows/GraphClust_2r_vrnafold_SHAPE.ga rename to workflows/extra-workflows/GraphClust_2r_vrnafold_SHAPE.ga diff --git a/workflows/GraphClust_3r_vrnafold.ga b/workflows/extra-workflows/GraphClust_3r_vrnafold.ga similarity index 100% rename from workflows/GraphClust_3r_vrnafold.ga rename to workflows/extra-workflows/GraphClust_3r_vrnafold.ga diff --git a/workflows/GraphClust_3r_vrnafold_SHAPE.ga b/workflows/extra-workflows/GraphClust_3r_vrnafold_SHAPE.ga similarity index 100% rename from workflows/GraphClust_3r_vrnafold_SHAPE.ga rename to workflows/extra-workflows/GraphClust_3r_vrnafold_SHAPE.ga From 759cb6ee6b16a86b6589eaae826cfb12808d268c Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Thu, 4 Jan 2018 04:08:22 +0100 Subject: [PATCH 10/11] Update tour data link --- tours/graphclust_step_by_step.yaml | 2 +- tours/graphclust_tutorial.yaml | 2 +- tours/graphclust_very_short.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tours/graphclust_step_by_step.yaml b/tours/graphclust_step_by_step.yaml index 449ba2f..abd5253 100644 --- a/tours/graphclust_step_by_step.yaml +++ b/tours/graphclust_step_by_step.yaml @@ -56,7 +56,7 @@ steps: intro: "Links Acquired !" position: "top" textinsert: - https://github.com/eteriSokhoyan/test-data/raw/master/cliques-low-representatives.fa + https://github.com/BackofenLab/docker-galaxy-graphclust/raw/master/sample_data/cliques-low-representatives.fa - title: "Data Acquisition" element: "button#btn-start" diff --git a/tours/graphclust_tutorial.yaml b/tours/graphclust_tutorial.yaml index 567aa3f..c96e2c3 100644 --- a/tours/graphclust_tutorial.yaml +++ b/tours/graphclust_tutorial.yaml @@ -81,7 +81,7 @@ steps: This file contains annotated RNAs with human origin from RFAM database, from a mixture of RNA families." position: "top" textinsert: - https://github.com/eteriSokhoyan/test-data/raw/master/cliques-low-representatives.fa + https://github.com/BackofenLab/docker-galaxy-graphclust/raw/master/sample_data/cliques-low-representatives.fa - title: "Data Acquisition" element: "button#btn-start" diff --git a/tours/graphclust_very_short.yaml b/tours/graphclust_very_short.yaml index c6aaaf9..a9e6a8d 100644 --- a/tours/graphclust_very_short.yaml +++ b/tours/graphclust_very_short.yaml @@ -61,7 +61,7 @@ steps: intro: "Links Acquired !" position: "top" textinsert: - https://github.com/eteriSokhoyan/test-data/raw/master/cliques-low-representatives.fa + https://github.com/BackofenLab/docker-galaxy-graphclust/raw/master/sample_data/cliques-low-representatives.fa - title: "Data Acquisition" element: "button#btn-start" From 0221279133c39d722dbdc3768a3c10115918ca10 Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Thu, 4 Jan 2018 04:18:12 +0100 Subject: [PATCH 11/11] Only add workflow of root dir --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d8c70f9..49c6e8b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,7 +20,7 @@ ADD ./tours/* $GALAXY_ROOT/config/plugins/tours/ ADD library_data.yaml $GALAXY_ROOT/library_data.yaml # Add workflows to the Docker image -ADD ./workflows/* $GALAXY_ROOT/workflows/ +ADD ./workflows/*.ga $GALAXY_ROOT/workflows/ # Download training data and populate the data library RUN startup_lite && \