changeset 0:ce9f11c6b94b draft

planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author scottx611x
date Tue, 04 Sep 2018 13:56:11 -0400
parents
children cbf8233bf744
files Kallisto_RNA-seq_(PE)_Quantification_-_Human.ga Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.ga Kallisto_RNA-seq_(PE)_Quantification_-_Zebrafish.ga Kallisto_RNA-seq_(SE)_Quantification_-_Human.ga Kallisto_RNA-seq_(SE)_Quantification_-_Mouse.ga Kallisto_RNA-seq_(SE)_Quantification_-_Zebrafish.ga repository_dependencies.xml
diffstat 7 files changed, 667 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Kallisto_RNA-seq_(PE)_Quantification_-_Human.ga	Tue Sep 04 13:56:11 2018 -0400
@@ -0,0 +1,108 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+                    "type": "tabular"
+                }, 
+                {
+                    "name": "pseudobam_output", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "fusion_output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 874, 
+                "top": 325.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionabundance_h5": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "abundance_h5"
+                }, 
+                "HideDatasetActionabundance_tab": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "abundance_tab"
+                }, 
+                "HideDatasetActionfusion_output": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "fusion_output"
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", 
+            "tool_shed_repository": {
+                "changeset_revision": "b818b23df1e0", 
+                "name": "kallisto_quant", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": null, \"bootstrap_samples\": \"\\\"0\\\"\", \"single_paired\": \"{\\\"fragment_length\\\": \\\"200\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"single_paired_selector\\\": \\\"single\\\", \\\"sd\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"mm10\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", 
+            "tool_version": "0.43.1.3", 
+            "type": "tool", 
+            "uuid": "c124061f-5652-4e12-878b-88ecdaf4cc09", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "pseudobam_output", 
+                    "uuid": "84016f1d-3195-49ae-8aad-764d3b1d2729"
+                }
+            ]
+        }
+    }, 
+    "uuid": "95467aa5-2868-4f50-a026-7f89be4306a8"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Kallisto_RNA-seq_(SE)_Quantification_-_Zebrafish.ga	Tue Sep 04 13:56:11 2018 -0400
@@ -0,0 +1,113 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "{ \n    \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Single-end reads are quantified against the danRer11 transcriptome.\", \n    \"file_relationship\": { \n        \"file_relationship\": {}, \n        \"value_type\": \"LIST\", \n        \"name\": \"List of FASTQ Files\", \n        \"input_files\": [ \n            { \n                \"allowed_filetypes\": [{\"name\": \"FASTQ\"}], \n                \"name\": \"Input File\", \n                \"description\": \"FASTQ File\" \n            } \n        ] \n    } \n}", 
+    "format-version": "0.1", 
+    "name": "Kallisto RNA-seq (SE) Quantification - Human", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "errors": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Input dataset collection", 
+            "outputs": [], 
+            "position": {
+                "left": 371.5, 
+                "top": 214
+            }, 
+            "tool_id": null, 
+            "tool_state": "{\"collection_type\": \"list\"}", 
+            "tool_version": null, 
+            "type": "data_collection_input", 
+            "uuid": "38a1eccd-850d-4b18-876c-097acf776154", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "51e4c27c-9b75-4306-b858-8ea222b2f4d4"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", 
+            "errors": null, 
+            "id": 1, 
+            "input_connections": {
+                "single_paired|reads": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Kallisto quant", 
+                    "name": "single_paired"
+                }
+            ], 
+            "label": null, 
+            "name": "Kallisto quant", 
+            "outputs": [
+                {
+                    "name": "abundance_h5", 
+                    "type": "h5"
+                }, 
+                {
+                    "name": "abundance_tab", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "pseudobam_output", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "fusion_output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1008, 
+                "top": 434.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionabundance_h5": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "abundance_h5"
+                }, 
+                "HideDatasetActionfusion_output": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "fusion_output"
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", 
+            "tool_shed_repository": {
+                "changeset_revision": "b818b23df1e0", 
+                "name": "kallisto_quant", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": null, \"bootstrap_samples\": \"\\\"0\\\"\", \"single_paired\": \"{\\\"fragment_length\\\": \\\"200\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"single_paired_selector\\\": \\\"single\\\", \\\"sd\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"hg38\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", 
+            "tool_version": "0.43.1.3", 
+            "type": "tool", 
+            "uuid": "068a2827-4c38-4aed-8a76-f1fb5f179e33", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "pseudobam_output", 
+                    "uuid": "1da5bcc0-11bd-4b2e-a625-4141f0ae0be8"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "abundance_tab", 
+                    "uuid": "e61317ef-a90d-4580-9295-47de567a2b3d"
+                }
+            ]
+        }
+    }, 
+    "uuid": "a1c133f3-2887-4ac7-b66a-c9ce07e74fc6"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Sep 04 13:56:11 2018 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Stem Cell Commons Kallisto workflows require kallisto_quant tool.">
+  <repository toolshed="https://toolshed.g2.bx.psu.edu" name="kallisto_quant" owner="iuc" changeset_revision="b818b23df1e0" />
+</repositories>