Mercurial > repos > galaxyp > proteogenomics_splice_junc_search_db
changeset 0:3e7ebf62c90f draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author | galaxyp |
---|---|
date | Tue, 10 May 2016 18:12:00 -0400 |
parents | |
children | |
files | Proteomics_Splice_DB_from_Paired_End_RNAseq.ga Proteomics_Splice_DB_from_Paired_End_RNAseq_cached_ref.ga Proteomics_Splice_DB_from_Single_End_RNAseq.ga Proteomics_Splice_DB_from_Single_End_RNAseq_cached_ref.ga repository_dependencies.xml |
diffstat | 5 files changed, 1590 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Proteomics_Splice_DB_from_Paired_End_RNAseq.ga Tue May 10 18:12:00 2016 -0400 @@ -0,0 +1,431 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Paired End \nRNAseq data", + "format-version": "0.1", + "name": "Proteomics Splice DB from Paired End RNAseq", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq left mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 186, + "top": 459 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c3fdc9d3-63ee-4cfb-81a4-75ac27d150c7" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq right mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 190, + "top": 527 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "14a32851-9e26-4eaf-b36c-0ab67e513d1d" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome GTF" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 192.5, + "top": 600 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome GTF\"}", + "tool_version": null, + "type": "data_input", + "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43" + } + ] + }, + "3": { + "annotation": "", + "content_id": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference Genome FASTA file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 523, + "top": 548 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference Genome FASTA file\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c98b5818-3d22-48f9-87bd-48ef64d41aeb" + } + ] + }, + "4": { + "annotation": "Allow novel junctions, not from the GTF", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 4, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "refGenomeSource|ownFile": { + "id": 3, + "output_name": "output" + }, + "singlePaired|input2": { + "id": 1, + "output_name": "output" + }, + "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 726, + "top": 259 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "deletions", + "uuid": "6eb54d42-20ff-4a15-baa3-9a85fe611b47" + }, + { + "label": null, + "output_name": "insertions", + "uuid": "8dae0352-0c26-43f3-9e90-8b5af6e11fbe" + }, + { + "label": null, + "output_name": "accepted_hits", + "uuid": "52a1f08e-c4ae-44c2-b50b-5b49200bad82" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "1f95f460-4b20-4ee0-b8d3-bd60c1d29c7e" + } + ] + }, + "5": { + "annotation": "Only look for supplied junctions", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 5, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "refGenomeSource|ownFile": { + "id": 3, + "output_name": "output" + }, + "singlePaired|input2": { + "id": 1, + "output_name": "output" + }, + "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 721, + "top": 658 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "deletions", + "uuid": "b253d572-820b-4a47-82b2-9dd687db6919" + }, + { + "label": null, + "output_name": "insertions", + "uuid": "6e5613af-9afc-4093-9825-158445322155" + }, + { + "label": null, + "output_name": "accepted_hits", + "uuid": "bb092754-4a16-42c5-a41c-60473fe7a636" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "d20c96cf-7e14-4dc3-88ad-8059ea05cd62" + } + ] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "id": 6, + "input_connections": { + "guided_junctions": { + "id": 5, + "output_name": "junctions" + }, + "input_bed": { + "id": 4, + "output_name": "junctions" + } + }, + "inputs": [], + "label": null, + "name": "Filter BED on splice junctions", + "outputs": [ + { + "name": "novel_junctions", + "type": "bed" + } + ], + "position": { + "left": 1014, + "top": 415 + }, + "post_job_actions": { + "HideDatasetActionnovel_junctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "novel_junctions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "Extract genomic DNA 1", + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "novel_junctions" + }, + "seq_source|ref_file": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1213, + "top": 621 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "2.2.3", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "out_file1", + "uuid": "fd68649b-1a31-4fb1-885a-92f374e4430f" + } + ] + }, + "8": { + "annotation": "Set the ID prefix for generated IDs when you intend to merge multiple samples from multiple fastq inputs to guarantee unique protein junction names.", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "id": 8, + "input_connections": { + "input": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + }, + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + } + ], + "label": null, + "name": "Translate BED Sequences", + "outputs": [ + { + "name": "translated_bed", + "type": "bed" + }, + { + "name": "output", + "type": "fasta" + } + ], + "position": { + "left": 1431.5, + "top": 451.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"\\\"\\\"\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde", + "workflow_outputs": [ + { + "label": null, + "output_name": "translated_bed", + "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f" + }, + { + "label": null, + "output_name": "output", + "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb" + } + ] + } + }, + "uuid": "e0cf1a1d-4678-47cd-af5d-e2896c27e35f" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Proteomics_Splice_DB_from_Paired_End_RNAseq_cached_ref.ga Tue May 10 18:12:00 2016 -0400 @@ -0,0 +1,401 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Paired End \nRNAseq data", + "format-version": "0.1", + "name": "Proteomics Splice DB from Paired End RNAseq cached ref", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq left mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 186, + "top": 459 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c3fdc9d3-63ee-4cfb-81a4-75ac27d150c7" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq right mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 190, + "top": 527 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "14a32851-9e26-4eaf-b36c-0ab67e513d1d" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome GTF" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 192.5, + "top": 600 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome GTF\"}", + "tool_version": null, + "type": "data_input", + "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43" + } + ] + }, + "3": { + "annotation": "Allow novel junctions, not from the GTF\n\nBe sure to select the correct Genome Reference", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 3, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "singlePaired|input2": { + "id": 1, + "output_name": "output" + }, + "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool TopHat for Illumina", + "name": "refGenomeSource" + } + ], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 726, + "top": 259 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "deletions", + "uuid": "1eb9eafa-90f7-4717-a196-4704592381e0" + }, + { + "label": null, + "output_name": "insertions", + "uuid": "92733c89-05ea-4815-96ba-7ab1d3f753d2" + }, + { + "label": null, + "output_name": "accepted_hits", + "uuid": "22eeb200-0a5b-4580-8572-777913cda04a" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "89706986-f95d-423a-b0ad-c616aa8e924e" + } + ] + }, + "4": { + "annotation": "Only look for supplied junctions\n\nBe sure to select the correct Genome Reference", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 4, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "singlePaired|input2": { + "id": 1, + "output_name": "output" + }, + "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool TopHat for Illumina", + "name": "refGenomeSource" + } + ], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 721, + "top": 658 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "deletions", + "uuid": "6937a7bd-c33d-4052-8594-50761dd454ea" + }, + { + "label": null, + "output_name": "insertions", + "uuid": "30e64406-f47d-476c-858b-4ba873c5486b" + }, + { + "label": null, + "output_name": "accepted_hits", + "uuid": "2fd2c931-de38-4950-b6db-dfe1c8407a00" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "e2d804b6-7bab-4746-92eb-58db4bcfed3f" + } + ] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "id": 5, + "input_connections": { + "guided_junctions": { + "id": 4, + "output_name": "junctions" + }, + "input_bed": { + "id": 3, + "output_name": "junctions" + } + }, + "inputs": [], + "label": null, + "name": "Filter BED on splice junctions", + "outputs": [ + { + "name": "novel_junctions", + "type": "bed" + } + ], + "position": { + "left": 1014, + "top": 415 + }, + "post_job_actions": { + "HideDatasetActionnovel_junctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "novel_junctions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "Extract genomic DNA 1", + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "novel_junctions" + } + }, + "inputs": [], + "label": null, + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1213, + "top": 621 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", + "tool_version": "2.2.3", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "7": { + "annotation": "Set the ID prefix for generated IDs \nwhen you intend to merge multiple samples from multiple fastq inputs", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "min_length" + }, + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + }, + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + } + ], + "label": null, + "name": "Translate BED Sequences", + "outputs": [ + { + "name": "translated_bed", + "type": "bed" + }, + { + "name": "output", + "type": "fasta" + } + ], + "position": { + "left": 1431.5, + "top": 451.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde", + "workflow_outputs": [ + { + "label": null, + "output_name": "translated_bed", + "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f" + }, + { + "label": "protein fasta", + "output_name": "output", + "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb" + } + ] + } + }, + "uuid": "7799d59b-149b-457c-a248-0ae65c1b8f63" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Proteomics_Splice_DB_from_Single_End_RNAseq.ga Tue May 10 18:12:00 2016 -0400 @@ -0,0 +1,393 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Single End RNAseq data", + "format-version": "0.1", + "name": "Proteomics Splice DB from Single End RNAseq cached ref", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq left mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 186, + "top": 459 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c3fdc9d3-63ee-4cfb-81a4-75ac27d150c7" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome GTF" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 192.5, + "top": 600 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome GTF\"}", + "tool_version": null, + "type": "data_input", + "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference Genome FASTA file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 523, + "top": 548 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference Genome FASTA file\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c98b5818-3d22-48f9-87bd-48ef64d41aeb" + } + ] + }, + "3": { + "annotation": "Allow novel junctions, not from the GTF", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 3, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "refGenomeSource|ownFile": { + "id": 2, + "output_name": "output" + }, + "singlePaired|sParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 726, + "top": 259 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"max_intron_length\\\": \\\"500000\\\", \\\"seg_length\\\": \\\"25\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "accepted_hits", + "uuid": "61a556d7-5ddb-4d3b-bceb-50816ea70122" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "946c9004-2239-4b2e-9bbe-2884f9a12b44" + } + ] + }, + "4": { + "annotation": "Only look for supplied junctions", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 4, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "refGenomeSource|ownFile": { + "id": 2, + "output_name": "output" + }, + "singlePaired|sParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 721, + "top": 658 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"max_intron_length\\\": \\\"500000\\\", \\\"seg_length\\\": \\\"25\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "accepted_hits", + "uuid": "92dbdf37-1195-44a1-8f3c-ed4709710a91" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "2058007a-c73f-4a0a-afd4-c093e13d6c83" + } + ] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "id": 5, + "input_connections": { + "guided_junctions": { + "id": 4, + "output_name": "junctions" + }, + "input_bed": { + "id": 3, + "output_name": "junctions" + } + }, + "inputs": [], + "label": null, + "name": "Filter BED on splice junctions", + "outputs": [ + { + "name": "novel_junctions", + "type": "bed" + } + ], + "position": { + "left": 1014, + "top": 415 + }, + "post_job_actions": { + "HideDatasetActionnovel_junctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "novel_junctions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "Extract genomic DNA 1", + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "novel_junctions" + }, + "seq_source|ref_file": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1213, + "top": 621 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "2.2.3", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + }, + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + } + ], + "label": null, + "name": "Translate BED Sequences", + "outputs": [ + { + "name": "translated_bed", + "type": "bed" + }, + { + "name": "output", + "type": "fasta" + } + ], + "position": { + "left": 1431.5, + "top": 451.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"\\\"\\\"\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde", + "workflow_outputs": [ + { + "label": null, + "output_name": "translated_bed", + "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f" + }, + { + "label": null, + "output_name": "output", + "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb" + } + ] + } + }, + "uuid": "37837db3-959f-4f56-bd46-c608ab1f8202" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Proteomics_Splice_DB_from_Single_End_RNAseq_cached_ref.ga Tue May 10 18:12:00 2016 -0400 @@ -0,0 +1,359 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Single End RNAseq data", + "format-version": "0.1", + "name": "Proteomics Splice DB from Single End RNAseq cached ref", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "RNA-Seq left mate pair fastq" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 186, + "top": 459 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}", + "tool_version": null, + "type": "data_input", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c3fdc9d3-63ee-4cfb-81a4-75ac27d150c7" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Reference genome GTF" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 192.5, + "top": 600 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Reference genome GTF\"}", + "tool_version": null, + "type": "data_input", + "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43" + } + ] + }, + "2": { + "annotation": "Allow novel junctions, not from the GTF", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 2, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "singlePaired|sParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool TopHat for Illumina", + "name": "refGenomeSource" + } + ], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 726, + "top": 259 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"max_intron_length\\\": \\\"500000\\\", \\\"seg_length\\\": \\\"25\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "accepted_hits", + "uuid": "61a556d7-5ddb-4d3b-bceb-50816ea70122" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "946c9004-2239-4b2e-9bbe-2884f9a12b44" + } + ] + }, + "3": { + "annotation": "Only look for supplied junctions", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "id": 3, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "singlePaired|sParams|own_junctions|gene_model_ann|gene_annotation_model": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool TopHat for Illumina", + "name": "refGenomeSource" + } + ], + "label": null, + "name": "TopHat for Illumina", + "outputs": [ + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + } + ], + "position": { + "left": 721, + "top": 658 + }, + "post_job_actions": { + "HideDatasetActiondeletions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deletions" + }, + "HideDatasetActioninsertions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "insertions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"max_intron_length\\\": \\\"500000\\\", \\\"seg_length\\\": \\\"25\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.5.0", + "type": "tool", + "uuid": "None", + "workflow_outputs": [ + { + "label": null, + "output_name": "accepted_hits", + "uuid": "92dbdf37-1195-44a1-8f3c-ed4709710a91" + }, + { + "label": null, + "output_name": "junctions", + "uuid": "2058007a-c73f-4a0a-afd4-c093e13d6c83" + } + ] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "id": 4, + "input_connections": { + "guided_junctions": { + "id": 3, + "output_name": "junctions" + }, + "input_bed": { + "id": 2, + "output_name": "junctions" + } + }, + "inputs": [], + "label": null, + "name": "Filter BED on splice junctions", + "outputs": [ + { + "name": "novel_junctions", + "type": "bed" + } + ], + "position": { + "left": 1014, + "top": 415 + }, + "post_job_actions": { + "HideDatasetActionnovel_junctions": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "novel_junctions" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1", + "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "Extract genomic DNA 1", + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "novel_junctions" + } + }, + "inputs": [], + "label": null, + "name": "Extract Genomic DNA", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1213, + "top": 621 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Extract genomic DNA 1", + "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", + "tool_version": "2.2.3", + "type": "tool", + "uuid": "None", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + }, + { + "description": "runtime parameter for tool Translate BED Sequences", + "name": "filter" + } + ], + "label": null, + "name": "Translate BED Sequences", + "outputs": [ + { + "name": "translated_bed", + "type": "bed" + }, + { + "name": "output", + "type": "fasta" + } + ], + "position": { + "left": 1431.5, + "top": 451.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0", + "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"\\\"\\\"\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde", + "workflow_outputs": [ + { + "label": null, + "output_name": "translated_bed", + "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f" + }, + { + "label": null, + "output_name": "output", + "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb" + } + ] + } + }, + "uuid": "4f5210d3-92c5-43ff-834b-e9b6dc85c0c0" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue May 10 18:12:00 2016 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<repositories description="This workflow requires a number of different repositories."> + <repository changeset_revision="2ad64c5bb5f4" name="tophat" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d723eb657f1d" name="translate_bed_sequences" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="915e5c5e02e6" name="filter_bed_on_splice_junctions" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>