# HG changeset patch
# User aaronpetkau
# Date 1436091621 14400
# Node ID 0d0e6bb421a4eef6e8bbca9cfc2b4ab3a951477a
# Parent 473e5ce08c42f50c0f8821ae74ab2f52495f86b2
Uploaded
diff -r 473e5ce08c42 -r 0d0e6bb421a4 assembly_single_end_workflow.ga
--- a/assembly_single_end_workflow.ga Sun Jul 05 06:08:56 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,214 +0,0 @@
-{
- "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
diff -r 473e5ce08c42 -r 0d0e6bb421a4 repository_definitions.xml
--- a/repository_definitions.xml Sun Jul 05 06:08:56 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-
-
-
-
-
-
-
diff -r 473e5ce08c42 -r 0d0e6bb421a4 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Sun Jul 05 06:20:21 2015 -0400
@@ -0,0 +1,7 @@
+
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