Mercurial > repos > aaronpetkau > assembly_single_end

changeset 2:89cd759a5da9 draft

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Uploaded
author aaronpetkau
date Sun, 05 Jul 2015 06:31:25 -0400
parents 0d0e6bb421a4
children f7cd57d1cfb0
files assembly_single_end_workflow.ga repository_dependencies.xml
diffstat 2 files changed, 214 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assembly_single_end_workflow.ga	Sun Jul 05 06:31:25 2015 -0400
@@ -0,0 +1,214 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "denovo assembly", 
+    "steps": {
+        "0": {
+            "annotation": "The input sequence reads.", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "The input sequence reads.", 
+                    "name": "sequence_reads"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"sequence_reads\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "7abd13c4-679c-4601-9bdd-4410cdacb932"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "libraries_0|files_0|file_type|unpaired_reads": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "spades", 
+            "outputs": [
+                {
+                    "name": "out_contigs", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "out_contig_stats", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "out_scaffolds", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "out_scaffold_stats", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "out_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/lionelguy/spades/spades/1.0", 
+            "tool_state": "{\"__page__\": 0, \"iontorrent\": \"\\\"False\\\"\", \"kmers\": \"\\\"21,33,55,77,99,127\\\"\", \"cov\": \"{\\\"state\\\": \\\"off\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"nanopore\": \"[]\", \"libraries\": \"[{\\\"lib_type\\\": \\\"paired_end\\\", \\\"__index__\\\": 0, \\\"orientation\\\": \\\"fr\\\", \\\"files\\\": [{\\\"file_type\\\": {\\\"type\\\": \\\"unpaired\\\", \\\"unpaired_reads\\\": null, \\\"__current_case__\\\": 2}, \\\"__index__\\\": 0}]}]\", \"onlyassembler\": \"\\\"False\\\"\", \"trustedcontigs\": \"[]\", \"pacbio\": \"[]\", \"sc\": \"\\\"False\\\"\", \"untrustedcontigs\": \"[]\", \"sanger\": \"[]\", \"careful\": \"\\\"True\\\"\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "44e3830f-f4ec-4ab0-8fbb-f8076c35e04b"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 1, 
+                    "output_name": "out_contig_stats"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Column Regex Find And Replace", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 731, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regexColumn1/0.1.0", 
+            "tool_state": "{\"__page__\": 0, \"field\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\"0.000000000000000001\\\", \\\"pattern\\\": \\\"^0$\\\"}]\", \"input\": \"null\"}", 
+            "tool_version": "0.1.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "59b56d9b-094b-41e8-9572-6e4708379e66"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "fasta_input": {
+                    "id": 1, 
+                    "output_name": "out_contigs"
+                }, 
+                "tab_input": {
+                    "id": 2, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Filter SPAdes repeats", 
+            "outputs": [
+                {
+                    "name": "output_with_repeats", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "output_without_repeats", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "repeat_sequences_only", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "discarded_sequences", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1036, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/aaronpetkau/filter_spades_repeats/filter_spades_repeat/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"len_cutoff\": \"\\\"1000\\\"\", \"rep_cutoff\": \"\\\"1.75\\\"\", \"__rerun_remap_job_id__\": null, \"keep_leftover\": \"\\\"yes\\\"\", \"tab_input\": \"null\", \"cov_len_cutoff\": \"\\\"5000\\\"\", \"print_summary\": \"\\\"yes\\\"\", \"cov_cutoff\": \"\\\"0.33\\\"\", \"fasta_input\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "19c772f8-7e42-4195-8cbb-bdccd2a5cedb"
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input": {
+                    "id": 3, 
+                    "output_name": "output_with_repeats"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "assemblystats", 
+            "outputs": [
+                {
+                    "name": "stats", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "sortedcontigs", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "histogrampng", 
+                    "type": "png"
+                }, 
+                {
+                    "name": "summedcontigspng", 
+                    "type": "png"
+                }, 
+                {
+                    "name": "histogramdata", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "summedcontigdata", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1320, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/aaronpetkau/assemblystats/assemblystats/1.0.2", 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"contig\\\"\", \"__rerun_remap_job_id__\": null, \"bucket\": \"\\\"False\\\"\", \"all_outputs\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "07c871e9-4509-4c84-a479-8b597774af0e"
+        }
+    }, 
+    "uuid": "5a9d63ba-cab7-4dc7-8cbc-2131d87a837d"
+}
\ No newline at end of file
--- a/repository_dependencies.xml	Sun Jul 05 06:20:21 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Set of tools for a de novo assembly workflow">
-	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="spades" owner="lionelguy" changeset_revision="21734680d921" />
-	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="regex_find_replace" owner="jjohnson" changeset_revision="9ea374bb0350" />
-	<repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="assemblystats" owner="aaronpetkau" changeset_revision="3ee4bb1fa3b4" />
-	<repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="filter_spades_repeats" owner="aaronpetkau" changeset_revision="11c6da8c33b6" />
-</repositories>