add workflow test for single-cell raceid tutorial

galaxyproject · Dec 13, 2024 · 15a43b2 · 15a43b2
1 parent e229155
commit 15a43b2
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diff --git a/topics/single-cell/tutorials/scrna-raceid/data-library.yaml b/topics/single-cell/tutorials/scrna-raceid/data-library.yaml
@@ -15,7 +15,7 @@ items:
     - name: 'DOI: 10.5281/zenodo.1511582'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/9d07494b-b15c-4a69-baf5-1e77087586b7/intestinalData.tsv
+      - url: https://zenodo.org/record/1511582/files/intestinalData.tsv
         src: url
         ext: tabular
         info: https://doi.org/10.5281/zenodo.1511582
diff --git a/topics/single-cell/tutorials/scrna-raceid/tutorial.md b/topics/single-cell/tutorials/scrna-raceid/tutorial.md
@@ -6,6 +6,10 @@ priority: 2
 redirect_from:
   - /topics/transcriptomics/tutorials/scrna-raceid/tutorial
 zenodo_link: 'https://zenodo.org/record/1511582'
+answer_histories:
+  - label: "UseGalaxy.eu"
+    history: https://usegalaxy.eu/u/videmp/h/downstream-single-cell-rna-analysis-with-raceid
+    date: 2024-12-12
 tags:
 questions:
   - What is normalisation and why is it necessary?
@@ -41,12 +45,15 @@ key_points:
   - RaceID can be used to cluster cells based on the their gene expression profiles
   - StemID describes a hierarchical relationship between clusters to find multipotent progenitor stem cells to provide an understanding of cell development
   - FateID predicts the potential lineages that cells within specific clusters are inclined towards
-contributors:
-  - mtekman
-  - astrovsky01
 
-gitter: Galaxy-Training-Network/galaxy-single-cell
+contributions:
+    authorship:
+        - mtekman
+        - astrovsky01
+    testing:
+        - pavanvidem
 
+gitter: Galaxy-Training-Network/galaxy-single-cell
 
 ---
 

diff --git a/topics/single-cell/tutorials/scrna-raceid/workflows/RaceID-Workflow-tests.yml b/topics/single-cell/tutorials/scrna-raceid/workflows/RaceID-Workflow-tests.yml
@@ -0,0 +1,19 @@
+- doc: Test outline for RaceID-Workflow
+  job:
+    Tabular Matrix:
+      class: File
+      location: https://zenodo.org/record/1511582/files/intestinalData.tsv
+      filetype: tabular
+  outputs:
+    outdiffgenes (Step 8):
+      asserts:
+        has_n_lines:
+          value: 11
+        has_text:
+          text: "Chmp1a"
+          text: "Dgat1"
+    outpdf (Step 9):
+      asserts:
+        has_size:
+          value: 1573003
+          delta: 31460
diff --git a/...s/scrna-raceid/workflows/main_workflow.ga → ...scrna-raceid/workflows/RaceID-Workflow.ga b/...s/scrna-raceid/workflows/main_workflow.ga → ...scrna-raceid/workflows/RaceID-Workflow.ga
@@ -1,8 +1,15 @@
 {
     "a_galaxy_workflow": "true",
     "annotation": "Downstream Single-cell RNA analysis with RaceID",
+    "comments": [],
     "format-version": "0.1",
     "name": "RaceID Workflow",
+    "source_metadata": {
+        "trs_server": "",
+        "trs_tool_id": "single-cell-scrna-raceid",
+        "trs_url": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-raceid/versions/main-workflow",
+        "trs_version_id": "main-workflow"
+    },
     "steps": {
         "0": {
             "annotation": "",
@@ -20,20 +27,15 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "bottom": 167.21666717529297,
-                "height": 48.96665954589844,
-                "left": 38.75,
-                "right": 198.75,
-                "top": 118.25000762939453,
-                "width": 160,
-                "x": 38.75,
-                "y": 118.25000762939453
+                "left": 0.0,
+                "top": 2.5
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false}",
+            "tool_state": "{\"optional\": false, \"tag\": null}",
             "tool_version": null,
             "type": "data_input",
             "uuid": "ba3fe014-c728-486e-8ce4-55be24df0682",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -75,21 +77,22 @@
                 }
             ],
             "position": {
-                "bottom": 410.7666702270508,
-                "height": 293.76666259765625,
-                "left": 272.5,
-                "right": 432.5,
-                "top": 117.00000762939453,
-                "width": 160,
-                "x": 272.5,
-                "y": 117.00000762939453
+                "left": 233.75,
+                "top": 1.25
             },
             "post_job_actions": {},
             "tool_id": "raceid_filtnormconf",
-            "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"filt\": {\"mintotal\": \"3000\", \"minexpr\": \"5\", \"minnumber\": \"5\", \"hist_geq_one\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"intable\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_shed_repository": {
+                "changeset_revision": "43c146e25a43",
+                "name": "raceid_filtnormconf",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"filt\": {\"mintotal\": \"3000\", \"minexpr\": \"5\", \"minnumber\": \"5\", \"hist_geq_one\": false, \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"intable\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "6fd8dbde-93d2-4903-865f-78cc3c2fa299",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -150,21 +153,22 @@
                 }
             ],
             "position": {
-                "bottom": 466.46668243408203,
-                "height": 350.7166748046875,
-                "left": 520,
-                "right": 680,
-                "top": 115.75000762939453,
-                "width": 160,
-                "x": 520,
-                "y": 115.75000762939453
+                "left": 481.25,
+                "top": 0.0
             },
             "post_job_actions": {},
             "tool_id": "raceid_clustering",
-            "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"clust\": {\"metric\": \"pearson\", \"funcluster\": \"kmedoids\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"extra\": {\"tablelim\": \"25\", \"plotlim\": \"10\", \"foldchange\": \"1.0\", \"pvalue\": \"0.01\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"outlier\": {\"outminc\": \"5\", \"outlg\": \"2\", \"final\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"tsne\": {\"perplexity\": \"30\", \"knn\": \"10\", \"umap_nn\": \"15\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_shed_repository": {
+                "changeset_revision": "a4b734cd253b",
+                "name": "raceid_clustering",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"clust\": {\"metric\": \"pearson\", \"funcluster\": \"kmedoids\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"extra\": {\"tablelim\": \"25\", \"plotlim\": \"10\", \"foldchange\": \"1.0\", \"pvalue\": \"0.01\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"outlier\": {\"outminc\": \"5\", \"outlg\": \"2\", \"final\": false, \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"tsne\": {\"perplexity\": \"30\", \"knn\": \"10\", \"umap_nn\": \"15\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "ca88c6cb-03e0-400c-8942-4c7ac0545a67",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -218,21 +222,22 @@
                 }
             ],
             "position": {
-                "bottom": 298.08333587646484,
-                "height": 179.8333282470703,
-                "left": 778.75,
-                "right": 938.75,
-                "top": 118.25000762939453,
-                "width": 160,
-                "x": 778.75,
-                "y": 118.25000762939453
+                "left": 740.0,
+                "top": 2.5
             },
             "post_job_actions": {},
             "tool_id": "raceid_trajectory",
-            "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"comppval\": {\"pthr\": \"0.01\", \"sensitive\": \"false\"}, \"compscore\": {\"nn\": \"1\", \"scthr\": \"0.0\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgraph\": {\"showcells\": \"false\", \"scthr\": \"0.0\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projback\": {\"pdishuf\": \"2000\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projcell\": {\"knn\": \"3\", \"cthr\": \"5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"use_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_shed_repository": {
+                "changeset_revision": "72979cac22b2",
+                "name": "raceid_trajectory",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"comppval\": {\"pthr\": \"0.01\", \"sensitive\": false}, \"compscore\": {\"nn\": \"1\", \"scthr\": \"0.0\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgraph\": {\"showcells\": false, \"scthr\": \"0.0\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projback\": {\"pdishuf\": \"2000\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projcell\": {\"knn\": \"3\", \"cthr\": \"5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"use_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "515732a4-cba5-402a-9cc8-11980c4815c6",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -271,21 +276,22 @@
                 }
             ],
             "position": {
-                "bottom": 512.9500045776367,
-                "height": 147.1999969482422,
-                "left": 773.75,
-                "right": 933.75,
-                "top": 365.75000762939453,
-                "width": 160,
-                "x": 773.75,
-                "y": 365.75000762939453
+                "left": 735.0,
+                "top": 250.0
             },
             "post_job_actions": {},
             "tool_id": "raceid_inspectclusters",
+            "tool_shed_repository": {
+                "changeset_revision": "41f34e925bd5",
+                "name": "raceid_inspectclusters",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
             "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"clusts_plot\": \"\"}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "727ee241-4de7-408f-867a-fc1ed21c23cb",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -324,21 +330,22 @@
                 }
             ],
             "position": {
-                "bottom": 712.9500045776367,
-                "height": 147.1999969482422,
-                "left": 773.75,
-                "right": 933.75,
-                "top": 565.7500076293945,
-                "width": 160,
-                "x": 773.75,
-                "y": 565.7500076293945
+                "left": 735.0,
+                "top": 450.0
             },
             "post_job_actions": {},
             "tool_id": "raceid_inspectclusters",
+            "tool_shed_repository": {
+                "changeset_revision": "41f34e925bd5",
+                "name": "raceid_inspectclusters",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
             "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"inspect_goi_genes\": \"Gstm3, St3gal4, Gna11\", \"inspect_goi_cells\": \"\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "6db63f68-65bc-4bb5-96a2-9d3e75712287",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -377,21 +384,22 @@
                 }
             ],
             "position": {
-                "bottom": 827.9499664306641,
-                "height": 147.1999969482422,
-                "left": 1035,
-                "right": 1195,
-                "top": 680.7499694824219,
-                "width": 160,
-                "x": 1035,
-                "y": 680.7499694824219
+                "left": 996.25,
+                "top": 564.9999618530273
             },
             "post_job_actions": {},
             "tool_id": "raceid_inspectclusters",
+            "tool_shed_repository": {
+                "changeset_revision": "41f34e925bd5",
+                "name": "raceid_inspectclusters",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
             "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"set_a\": {\"name_set\": \"Cells in 1\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"1\"}}, \"set_b\": {\"name_set\": \"Cells in 3\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"3\"}}, \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "57c7332a-c6f5-484f-8a5c-d5467d320e72",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -434,21 +442,22 @@
                 }
             ],
             "position": {
-                "bottom": 372.61666107177734,
-                "height": 253.1166534423828,
-                "left": 1041.25,
-                "right": 1201.25,
-                "top": 119.50000762939453,
-                "width": 160,
-                "x": 1041.25,
-                "y": 119.50000762939453
+                "left": 1002.5,
+                "top": 3.75
             },
             "post_job_actions": {},
             "tool_id": "raceid_inspecttrajectory",
+            "tool_shed_repository": {
+                "changeset_revision": "c8434a623268",
+                "name": "raceid_inspecttrajectory",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
             "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"trjsid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"i\": \"3\", \"br\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "4a519b59-2319-4811-969e-3b872f95c377",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -492,21 +501,22 @@
                 }
             ],
             "position": {
-                "bottom": 625.5833358764648,
-                "height": 179.8333282470703,
-                "left": 1040,
-                "right": 1200,
-                "top": 445.75000762939453,
-                "width": 160,
-                "x": 1040,
-                "y": 445.75000762939453
+                "left": 1001.25,
+                "top": 330.0
             },
             "post_job_actions": {},
             "tool_id": "raceid_inspecttrajectory",
+            "tool_shed_repository": {
+                "changeset_revision": "c8434a623268",
+                "name": "raceid_inspecttrajectory",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
             "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"cellsfromz\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}, \"som\": {\"doit\": \"no\", \"__current_case__\": 0}}}, \"trjsid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.2.3+galaxy0",
             "type": "tool",
             "uuid": "883ffd05-1545-449f-8028-c45c0f9edfd5",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": null,
@@ -526,5 +536,5 @@
         "single-cell"
     ],
     "uuid": "48285e72-0fb6-4cd6-a329-73d0e28effea",
-    "version": 1
+    "version": 0
 }
diff --git a/topics/single-cell/tutorials/scrna-raceid/workflows/index.md b/topics/single-cell/tutorials/scrna-raceid/workflows/index.md
@@ -1,5 +1,5 @@
 ---
 layout: workflow-list
 redirect_from:
-  - /topics/transcriptomics/tutorials/scrna-raceid/workflows/index
+  - /topics/single-cell/tutorials/scrna-raceid/workflows/index
 ---