Merge pull request #2021 from cat-bro/update_maxquant_workflow_with_h…

…istogram_1_0_4_and_test

update maxquant workflow to use histogram version to 1.0.4, add test

topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph-test.yml

@@ -0,0 +1,17 @@
+- doc: Test for debruijn-graph.ga
+  job:
+    mutant_R1:
+      class: File
+      location: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R1.fastq
+    mutant_R2:
+      class: File
+      location: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R2.fastq
+  outputs:
+    fasta_stats_spades:
+      asserts:
+        has_text_matching:
+          expression: 'len_N50\s*132559'
+    fasta_stats_velvet:
+      asserts:
+        has_text_matching:
+          expression: 'GC_content\s*33.6'

topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free-test.yml

@@ -0,0 +1,20 @@
+- doc: Test for maxquant_label_free.ga
+  job:
+    Fasta file:
+      class: File
+      path: todo_test_data_path.ext
+    sample1:
+      class: File
+      path: todo_test_data_path.ext
+    sample2:
+      class: File
+      path: todo_test_data_path.ext
+  outputs:
+    column_maker_out1:
+      asserts:
+        has_text:
+          text: "kappa"
+    histogram_out:
+      asserts:
+        has_text:
+          text: "PDF"

topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga

@@ -113,7 +113,7 @@
     },
     "11": {
       "annotation": "",
-      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
       "errors": null,
       "id": 11,
       "input_connections": {
@@ -136,20 +136,20 @@
         "top": 509.16668701171875
       },
       "post_job_actions": {},
-      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3",
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
       "tool_shed_repository": {
-        "changeset_revision": "549d2cb4c6f2",
-        "name": "dna_filtering",
+        "changeset_revision": "6f134426c2b0",
+        "name": "histogram",
         "owner": "devteam",
         "tool_shed": "toolshed.g2.bx.psu.edu"
       },
       "tool_state": "{\"xlab\": \"\\\"log2 Fold Change\\\"\", \"density\": \"\\\"true\\\"\", \"__page__\": null, \"breaks\": \"\\\"0\\\"\", \"numerical_column\": \"\\\"6\\\"\", \"frequency\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"title\": \"\\\"Histogram\\\"\", \"__rerun_remap_job_id__\": null}",
-      "tool_version": "1.0.3",
+      "tool_version": "1.0.4",
       "type": "tool",
       "uuid": "4b5c9a13-067f-49d1-90f8-7d501ef81075",
       "workflow_outputs": [
         {
-          "label": null,
+          "label": "histogram_out",
           "output_name": "out_file1",
           "uuid": "74dcd462-de85-4b78-8549-4309be2a1d91"
         }
@@ -437,7 +437,7 @@
       "uuid": "fc27e1b8-a61a-4393-b4f8-597a09619088",
       "workflow_outputs": [
         {
-          "label": null,
+          "label": "column_maker_out1",
           "output_name": "out_file1",
           "uuid": "5587fe84-c203-432d-bfeb-aabb9a18b921"
         }