changeset 0:0b6e9cc279fc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/apostl commit 79aa418c07e54b5f152681452767f7c8a40379b6
author galaxyp
date Thu, 11 May 2017 14:52:17 -0400
parents
children
files Galaxy-Workflow-APOSTL_Workflow.ga repository_dependencies.xml
diffstat 2 files changed, 1486 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-APOSTL_Workflow.ga	Thu May 11 14:52:17 2017 -0400
@@ -0,0 +1,1477 @@
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+                    "action_type": "HideDatasetAction", 
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_zip"
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+                "RenameDatasetActionoutput_certificate": {
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+            "inputs": [
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+                    "description": "runtime parameter for tool Peptide Shaker", 
+                    "name": "searchgui_input"
+                }
+            ], 
+            "label": null, 
+            "name": "Peptide Shaker", 
+            "outputs": [
+                {
+                    "name": "mzidentML", 
+                    "type": "mzid"
+                }, 
+                {
+                    "name": "output_cps", 
+                    "type": "peptideshaker_archive"
+                }, 
+                {
+                    "name": "output_zip", 
+                    "type": "zip"
+                }, 
+                {
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+                    "type": "txt"
+                }, 
+                {
+                    "name": "output_hierarchical", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_psm_phosphorylation", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_psm", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_extended_psm", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_peptides_phosphorylation", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_peptides", 
+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "tabular"
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+                {
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+                    "type": "tabular"
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+                    "output_name": "output_cps"
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+                "HideDatasetActionoutput_extended_psm": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_extended_psm"
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+                "HideDatasetActionoutput_hierarchical": {
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+                    "action_type": "HideDatasetAction", 
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+                "HideDatasetActionoutput_peptides": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_peptides"
+                }, 
+                "HideDatasetActionoutput_peptides_phosphorylation": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_peptides_phosphorylation"
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+                "HideDatasetActionoutput_proteins_phosphorylation": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_proteins_phosphorylation"
+                }, 
+                "HideDatasetActionoutput_psm_phosphorylation": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_psm_phosphorylation"
+                }, 
+                "HideDatasetActionoutput_zip": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_zip"
+                }, 
+                "RenameDatasetActionoutput_certificate": {
+                    "action_arguments": {
+                        "newname": "PeptideShaker Summary Report: 04112012_JL_HCC827_GFP_TAP_2_run1"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_certificate"
+                }, 
+                "RenameDatasetActionoutput_proteins": {
+                    "action_arguments": {
+                        "newname": "PeptideShaker Protein Report: 04112012_JL_HCC827_GFP_TAP_2_run1"
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+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_proteins"
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+                "RenameDatasetActionoutput_psm": {
+                    "action_arguments": {
+                        "newname": "PeptideShaker PSM Report: 04112012_JL_HCC827_GFP_TAP_2_run1"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_psm"
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+            "input_connections": {
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+                    "output_name": "output"
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+                    "output_name": "output"
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+                    "output_name": "output_proteins"
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+                "type_select|protein_inputs_1|protein_file": {
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+                    "output_name": "output_proteins"
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+                "type_select|protein_inputs_2|protein_file": {
+                    "id": 13, 
+                    "output_name": "output_proteins"
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+                "type_select|protein_inputs_3|protein_file": {
+                    "id": 12, 
+                    "output_name": "output_proteins"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAINT pre-processing", 
+                    "name": "type_select"
+                }, 
+                {
+                    "description": "runtime parameter for tool SAINT pre-processing", 
+                    "name": "type_select"
+                }
+            ], 
+            "label": null, 
+            "name": "SAINT pre-processing", 
+            "outputs": [
+                {
+                    "name": "Inter_file", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "Prey_file", 
+                    "type": "txt"
+                }, 
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+                    "type": "txt"
+                }
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+                "top": 394
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionBait_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "Bait_file"
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+                "HideDatasetActionInter_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "Inter_file"
+                }, 
+                "HideDatasetActionPrey_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "Prey_file"
+                }
+            }, 
+            "tool_errors": null, 
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+                "owner": "bornea", 
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+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "uuid": "7504f5ce-684d-46f6-bc00-d4b8eaf87b3a", 
+            "workflow_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/query_crapome/CRAPomeQuery/1.0.0", 
+            "id": 17, 
+            "input_connections": {
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+                "input": {
+                    "id": 16, 
+                    "output_name": "Prey_file"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Query CRAPome", 
+                    "name": "input"
+                }, 
+                {
+                    "description": "runtime parameter for tool Query CRAPome", 
+                    "name": "fasta_db"
+                }
+            ], 
+            "label": null, 
+            "name": "Query CRAPome", 
+            "outputs": [
+                {
+                    "name": "CrapomeFile", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1267, 
+                "top": 723
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionCrapomeFile": {
+                    "action_arguments": {
+                        "newname": "CRAPome File Output"
+                    }, 
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+                    "output_name": "CrapomeFile"
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+            "tool_shed_repository": {
+                "changeset_revision": "f1459638e1bc", 
+                "name": "query_crapome", 
+                "owner": "bornea", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fasta_db\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"species\": \"\\\"HUMAN\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "uuid": "16096e29-d534-4a6d-9627-e7e287798c71", 
+            "workflow_outputs": [
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+                    "output_name": "CrapomeFile", 
+                    "uuid": "1f90a8ba-22ee-45c4-9018-98a153162583"
+                }
+            ]
+        }, 
+        "18": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", 
+            "id": 18, 
+            "input_connections": {
+                "bait_input": {
+                    "id": 16, 
+                    "output_name": "Bait_file"
+                }, 
+                "inter_input": {
+                    "id": 16, 
+                    "output_name": "Inter_file"
+                }, 
+                "prey_input": {
+                    "id": 16, 
+                    "output_name": "Prey_file"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAINTexpress", 
+                    "name": "go_file"
+                }, 
+                {
+                    "description": "runtime parameter for tool SAINTexpress", 
+                    "name": "bait_input"
+                }, 
+                {
+                    "description": "runtime parameter for tool SAINTexpress", 
+                    "name": "inter_input"
+                }, 
+                {
+                    "description": "runtime parameter for tool SAINTexpress", 
+                    "name": "prey_input"
+                }
+            ], 
+            "label": null, 
+            "name": "SAINTexpress", 
+            "outputs": [
+                {
+                    "name": "SAINT_output", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1763.5, 
+                "top": 524
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionSAINT_output": {
+                    "action_arguments": {
+                        "newname": "SAINT Output File"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "SAINT_output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "67631a640534", 
+                "name": "saintexpress", 
+                "owner": "bornea", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"rep_num\": \"\\\"100\\\"\", \"__page__\": 0, \"go_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bait_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vc_bool\": \"\\\"false\\\"\", \"inter_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"go_bool\": \"\\\"false\\\"\", \"prey_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vc_num\": \"\\\"1\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "uuid": "86e2c9ce-be72-496b-84c2-7e3027d0187e", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "SAINT_output", 
+                    "uuid": "f4c612f6-d132-444f-9474-f95f7b968382"
+                }
+            ]
+        }
+    }, 
+    "uuid": "4f118197-8eee-42d5-ba46-3abfcb3f127b"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu May 11 14:52:17 2017 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<repositories description="This workflow requires a number of different repositories.">
+    <repository changeset_revision="f1459638e1bc" name="query_crapome" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="6ad498eac0e2" name="saint_preprocessing" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="67631a640534" name="saintexpress" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="19ee2e85931a" name="dbbuilder" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="2904d46167da" name="fasta_merge_files_and_filter_unique_sequences" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="7f2aeb19650f" name="peptideshaker" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>