Mercurial > repos > aaronpetkau > assembly_single_end
changeset 7:37f2f0461661 draft default tip
Uploaded
| author | aaronpetkau |
|---|---|
| date | Sun, 05 Jul 2015 09:51:33 -0400 |
| parents | cf29452b3583 |
| children | |
| files | assembly_single_end_workflow.ga repository_dependencies.xml |
| diffstat | 2 files changed, 316 insertions(+), 0 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 09:51:33 2015 -0400 @@ -0,0 +1,309 @@ +{ + "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": "160ccf74-1495-499a-a3a1-e62f50cf4cdb" + }, + "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": { + "HideDatasetActionout_contig_stats": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_contig_stats" + }, + "HideDatasetActionout_contigs": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_contigs" + }, + "HideDatasetActionout_log": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_log" + }, + "HideDatasetActionout_scaffold_stats": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_scaffold_stats" + }, + "HideDatasetActionout_scaffolds": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_scaffolds" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.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": "ebef4b3f-b086-4559-9e25-2dccf3eae18e" + }, + "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": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "testtoolshed.g2.bx.psu.edu/repos/aaronpetkau/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": "1f0689d0-3cb8-4985-a89a-ebc935f40100" + }, + "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": { + "HideDatasetActiondiscarded_sequences": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "discarded_sequences" + }, + "HideDatasetActionoutput_without_repeats": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_without_repeats" + }, + "HideDatasetActionrepeat_sequences_only": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "repeat_sequences_only" + }, + "RenameDatasetActionoutput_with_repeats": { + "action_arguments": { + "newname": "contigs_with_repeats.fasta" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_with_repeats" + }, + "RenameDatasetActionsummary": { + "action_arguments": { + "newname": "filter_spades_repeats_summary.txt" + }, + "action_type": "RenameDatasetAction", + "output_name": "summary" + } + }, + "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": "2fe5db93-8232-4248-b3c5-8ad71214762c" + }, + "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": { + "HideDatasetActionhistogramdata": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "histogramdata" + }, + "HideDatasetActionhistogrampng": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "histogrampng" + }, + "HideDatasetActionsortedcontigs": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "sortedcontigs" + }, + "HideDatasetActionsummedcontigdata": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "summedcontigdata" + }, + "HideDatasetActionsummedcontigspng": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "summedcontigspng" + }, + "RenameDatasetActionstats": { + "action_arguments": { + "newname": "contigs_with_repeats_stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "stats" + } + }, + "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": "8af6f2d0-048d-4ea9-b60d-5c4e4e82d52d" + } + }, + "uuid": "e6768ba7-13c9-4c9e-8593-258fc51351eb" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sun Jul 05 09:51:33 2015 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<repositories description="Set of tools for a de novo assembly workflow"> + <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="spades" owner="lionelguy" changeset_revision="0730381ba8bd" /> + <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="regex_find_replace" owner="aaronpetkau" changeset_revision="a8bd03327fb7" /> + <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>