Merge pull request #177 from planemo-autoupdate/workflows/data-fetchi…

…ng/parallel-accession-download Updating workflows/data-fetching/parallel-accession-download from 0.1.3 to 0.1.4
galaxyproject · Sep 5, 2023 · b01ea1f · b01ea1f
2 parents d1f2a6a + b459dd5
commit b01ea1f
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diff --git a/workflows/data-fetching/parallel-accession-download/.dockstore.yml b/workflows/data-fetching/parallel-accession-download/.dockstore.yml
@@ -1,7 +1,13 @@
 version: 1.2
 workflows:
 - name: main
-  primaryDescriptorPath: /parallel-accession-download.ga
   subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /parallel-accession-download.ga
   testParameterFiles:
   - /parallel-accession-download-tests.yml
+  authors:
+  - name: Marius van den Beek
+    orcid: 0000-0002-9676-7032
+  - name: IWC
+    url: https://github.com/galaxyproject/iwc
diff --git a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.4] 2023-02-17
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0`
+
 ## [0.1.3] 2022-02-04
 
 ### Automatic update

diff --git a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1.3",
+    "release": "0.1.4",
     "name": "Parallel Accession Download",
     "steps": {
         "0": {
@@ -34,20 +34,15 @@
             "name": "Input dataset",
             "outputs": [],
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-                "left": 387.4250183105469,
-                "right": 587.4250183105469,
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-                "width": 200,
-                "x": 387.4250183105469,
-                "y": 573.3875122070312
+                "left": 0.0,
+                "top": 27.0
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"txt\"]}",
+            "tool_state": "{\"optional\": false, \"format\": [\"txt\"], \"tag\": null}",
             "tool_version": null,
             "type": "data_input",
             "uuid": "e9e5605e-29e1-4f90-9693-0e40a2ddfd8f",
+            "when": null,
             "workflow_outputs": []
         },
         "1": {
@@ -71,14 +66,8 @@
                 }
             ],
             "position": {
-                "bottom": 851.4000244140625,
-                "height": 132,
-                "left": 533.9375,
-                "right": 733.9375,
-                "top": 719.4000244140625,
-                "width": 200,
-                "x": 533.9375,
-                "y": 719.4000244140625
+                "left": 146.51248168945312,
+                "top": 173.01251220703125
             },
             "post_job_actions": {
                 "HideDatasetActionlist_output_txt": {
@@ -98,6 +87,7 @@
             "tool_version": "0.5.0",
             "type": "tool",
             "uuid": "f8d776ff-e1ba-4bde-9b4b-392d825fd2b7",
+            "when": null,
             "workflow_outputs": []
         },
         "2": {
@@ -121,14 +111,8 @@
                 }
             ],
             "position": {
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-                "x": 725.4625244140625,
-                "y": 546.3875122070312
+                "left": 338.0375061035156,
+                "top": 0.0
             },
             "post_job_actions": {
                 "HideDatasetActiontext_param": {
@@ -138,15 +122,16 @@
                 }
             },
             "tool_id": "param_value_from_file",
-            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"text\", \"remove_newlines\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"text\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.1.0",
             "type": "tool",
             "uuid": "570d0317-259f-42b1-91f4-74f050e754b5",
+            "when": null,
             "workflow_outputs": []
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -177,14 +162,8 @@
                 }
             ],
             "position": {
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-                "left": 992.3500366210938,
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-                "top": 647.3624877929688,
-                "width": 200,
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+                "left": 604.9250183105469,
+                "top": 100.9749755859375
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             "post_job_actions": {
                 "HideDatasetActionlist_paired": {
@@ -208,17 +187,18 @@
                     "output_name": "output_collection_other"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "83c7d564b128",
+                "changeset_revision": "6ea73833cf67",
                 "name": "sra_tools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"input\": {\"input_select\": \"accession_number\", \"__current_case__\": 0, \"accession\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.11.0+galaxy1",
+            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": true}, \"input\": {\"input_select\": \"accession_number\", \"__current_case__\": 0, \"accession\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.0.5+galaxy0",
             "type": "tool",
             "uuid": "4d328e7b-df7d-4d3e-a60f-1ea12925f317",
+            "when": null,
             "workflow_outputs": []
         },
         "4": {
@@ -242,14 +222,8 @@
                 }
             ],
             "position": {
-                "bottom": 768.3624877929688,
-                "height": 112,
-                "left": 1319.425048828125,
-                "right": 1519.425048828125,
-                "top": 656.3624877929688,
-                "width": 200,
-                "x": 1319.425048828125,
-                "y": 656.3624877929688
+                "left": 932.0000305175781,
+                "top": 109.9749755859375
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             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -265,6 +239,7 @@
             "tool_version": "1.1.0",
             "type": "tool",
             "uuid": "924d2152-5640-40cd-bec3-0ced45469d84",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "Paired End Reads",
@@ -294,14 +269,8 @@
                 }
             ],
             "position": {
-                "bottom": 911.4125366210938,
-                "height": 112,
-                "left": 1326.4749755859375,
-                "right": 1526.4749755859375,
-                "top": 799.4125366210938,
-                "width": 200,
-                "x": 1326.4749755859375,
-                "y": 799.4125366210938
+                "left": 939.0499572753906,
+                "top": 253.0250244140625
             },
             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -317,6 +286,7 @@
             "tool_version": "1.1.0",
             "type": "tool",
             "uuid": "946d9610-c363-4915-b93a-f074169ef812",
+            "when": null,
             "workflow_outputs": [
                 {
                     "label": "Single End Reads",

diff --git a/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq b/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq
@@ -1,10 +1,12 @@
-@SRR044777.1 F47USSH02H1LGA length=160
+@F47USSH02H1LGA/4
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+SRR044777.1 F47USSH02H1LGA length=160
++
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-@SRR044777.2 F47USSH02GNP1D length=320
+@F47USSH02GNP1D/4
 CACGTAGTTAGCCGGTGCTTATTCTTCCGGTACCGTCAGCACGCAATGGTATTAACATCGCGCTTTTCTTCCCGGACAAAAGTCCTTTACAACCCGAAGGCCTTCTTCAGACACGCGGCATGGCTGGATCAGGGTTGCCCCCATTGTCCAAAATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCGGATCATCCTCTCAGACCCGCTACTGATCGTCGCCTTGGTAGGCCTTTACCCCACCAACCAGCTAATCAGATATCGGCCGCTCAAACAGCGCAAGGCACACAGGGGATAGGN
-+SRR044777.2 F47USSH02GNP1D length=320
++
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAAAAIIIHCCCCII@@@@IIIIHHHIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIII?????IIIIIII@@@@HH6666IFIIIIIIIIHHHIIIIIIIIIIHHHIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIIIIIIIIIIIIIIIIIIII??===?@B>>IDCIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHHIIIIII@@@@HIIII!
-@SRR044777.3 F47USSH02JNWNH length=78
+@F47USSH02JNWNH/4
 GGCCATGCCTGTACCTGGGGTCCCTACTGAGCCAGGATCAAACTCTCTGAGACTGCCAAGGCACACAGGGGGATAGGN
++
+AAIIIIIIIIIIIIIIACCCIHHHIIIIIIIIHHHHIIIHHHIIIIIIIIIIIIICCCCEAIIBB;4-----8<=<<!
diff --git a/workflows/data-fetching/parallel-accession-download/test-data/SRR11953971_1_head.fastq b/workflows/data-fetching/parallel-accession-download/test-data/SRR11953971_1_head.fastq
@@ -1,10 +1,12 @@
-@SRR11953971.1 1 length=101
+@1/1
 GATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCG
-+SRR11953971.1 1 length=101
++
 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
-@SRR11953971.2 2 length=101
+@2/1
 GTGTAGAAGGCTCGAACGCAGTGACGAAGCTGGACGTATCCGCCGACCGGTAAAGGGTAAGGGTCTCAATGGCGTTACACGTAACAGCTCGACTGAACGCT
-+SRR11953971.2 2 length=101
++
 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
-@SRR11953971.3 3 length=101
+@3/1
 GTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGCTGTCTCTTATACACATCTCC
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF
diff --git a/workflows/data-fetching/parallel-accession-download/test-data/SRR11953971_2_head.fastq b/workflows/data-fetching/parallel-accession-download/test-data/SRR11953971_2_head.fastq
@@ -1,10 +1,12 @@
-@SRR11953971.1 1 length=101
+@1/2
 TCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCAGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGA
-+SRR11953971.1 1 length=101
++
 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
-@SRR11953971.2 2 length=101
+@2/2
 GGAAATGAACTATATCGTAACCAAGCCGGGTAGCTGCTGTGGTGCTAGACTAGATGTTAGCGTTCAGTCGAGCTGTTACGTGTAACGCCATTGAGACCCTT
-+SRR11953971.2 2 length=101
++
 FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFF
-@SRR11953971.3 3 length=101
+@3/2
 CACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACCTGTCTCTTATACACATCTGA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF