Mercurial > repos > stemcellcommons > rnaseq_workflows
changeset 0:cbd6667ca478 draft
Initial upload
| author | stemcellcommons |
|---|---|
| date | Wed, 20 Jul 2016 16:58:05 -0400 |
| parents | |
| children | ba1b76257fa5 |
| files | RNA-seq_paired_end_with_TopHat_-_hg19.ga RNA-seq_paired_end_with_TopHat_-_mm10.ga RNA-seq_single_end_with_TopHat_-_hg19.ga RNA-seq_single_end_with_TopHat_-_mm10.ga |
| diffstat | 4 files changed, 992 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNA-seq_paired_end_with_TopHat_-_hg19.ga Wed Jul 20 16:58:05 2016 -0400 @@ -0,0 +1,281 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"forward_reads\", \"set2\": \"reverse_reads\"}]}", + "format-version": "0.1", + "name": "RNA-seq paired end with TopHat - hg19", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "forward_reads" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 207, + "top": 300 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"forward_reads\"}", + "tool_version": null, + "type": "data_input", + "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "reverse_reads" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 205, + "top": 437 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"reverse_reads\"}", + "tool_version": null, + "type": "data_input", + "uuid": "d2dbe3db-13ca-4155-a60a-cf408e53cb3a", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 2, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 455.5, + "top": 259 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 3, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 456.5, + "top": 475 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "7b504a0d-37d1-4a2c-9cba-0cc138331375", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "id": 4, + "input_connections": { + "paired_end|paired_input_type_conditional|fastq_r1_in": { + "id": 2, + "output_name": "output_file" + }, + "paired_end|paired_input_type_conditional|fastq_r2_in": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Trimmomatic", + "outputs": [ + { + "name": "fastq_out_paired", + "type": "input" + }, + { + "name": "fastq_out_unpaired", + "type": "input" + }, + { + "name": "fastq_out_r1_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r1_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out", + "type": "fastqsanger" + } + ], + "position": { + "left": 791, + "top": 282 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"seed_mismatches\\\": \\\"2\\\", \\\"adapter_fasta\\\": \\\"TruSeq3-SE.fa\\\", \\\"__current_case__\\\": 0, \\\"palindrome_clip_threshold\\\": \\\"30\\\", \\\"do_illuminaclip\\\": \\\"True\\\", \\\"simple_clip_threshold\\\": \\\"10\\\"}\"}", + "tool_version": "0.32.3", + "type": "tool", + "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", + "workflow_outputs": [] + }, + "5": { + "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "id": 5, + "input_connections": { + "singlePaired|input1": { + "id": 4, + "output_name": "fastq_out_r1_paired" + }, + "singlePaired|input2": { + "id": 4, + "output_name": "fastq_out_r2_paired" + } + }, + "inputs": [], + "label": null, + "name": "TopHat", + "outputs": [ + { + "name": "align_summary", + "type": "txt" + }, + { + "name": "fusions", + "type": "tabular" + }, + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + }, + { + "name": "unmapped", + "type": "bam" + } + ], + "position": { + "left": 1141, + "top": 279 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 2}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"output_unmapped\\\": \\\"False\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": \\\"hg19_genes.gtf\\\", \\\"use_annotations\\\": \\\"indexed\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "2.1.0", + "type": "tool", + "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", + "workflow_outputs": [] + }, + "6": { + "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "id": 6, + "input_connections": { + "alignments": { + "id": 5, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output", + "type": "tabular" + }, + { + "name": "output_summary", + "type": "tabular" + } + ], + "position": { + "left": 1441, + "top": 388 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/hg19_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.4.6.p5", + "type": "tool", + "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", + "workflow_outputs": [] + } + }, + "uuid": "3688391c-e028-4483-94a2-c70422e5ffdb" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNA-seq_paired_end_with_TopHat_-_mm10.ga Wed Jul 20 16:58:05 2016 -0400 @@ -0,0 +1,281 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"forward_reads\", \"set2\": \"reverse_reads\"}]}", + "format-version": "0.1", + "name": "RNA-seq paired end with TopHat - mm10", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "forward_reads" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 207, + "top": 300 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"forward_reads\"}", + "tool_version": null, + "type": "data_input", + "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "reverse_reads" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 205, + "top": 437 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"reverse_reads\"}", + "tool_version": null, + "type": "data_input", + "uuid": "d2dbe3db-13ca-4155-a60a-cf408e53cb3a", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 2, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 455.5, + "top": 259 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 3, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 456.5, + "top": 475 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "7b504a0d-37d1-4a2c-9cba-0cc138331375", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "id": 4, + "input_connections": { + "paired_end|paired_input_type_conditional|fastq_r1_in": { + "id": 2, + "output_name": "output_file" + }, + "paired_end|paired_input_type_conditional|fastq_r2_in": { + "id": 3, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Trimmomatic", + "outputs": [ + { + "name": "fastq_out_paired", + "type": "input" + }, + { + "name": "fastq_out_unpaired", + "type": "input" + }, + { + "name": "fastq_out_r1_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r1_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out", + "type": "fastqsanger" + } + ], + "position": { + "left": 791, + "top": 282 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"seed_mismatches\\\": \\\"2\\\", \\\"adapter_fasta\\\": \\\"TruSeq3-SE.fa\\\", \\\"__current_case__\\\": 0, \\\"palindrome_clip_threshold\\\": \\\"30\\\", \\\"do_illuminaclip\\\": \\\"True\\\", \\\"simple_clip_threshold\\\": \\\"10\\\"}\"}", + "tool_version": "0.32.3", + "type": "tool", + "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", + "workflow_outputs": [] + }, + "5": { + "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "id": 5, + "input_connections": { + "singlePaired|input1": { + "id": 4, + "output_name": "fastq_out_r1_paired" + }, + "singlePaired|input2": { + "id": 4, + "output_name": "fastq_out_r2_paired" + } + }, + "inputs": [], + "label": null, + "name": "TopHat", + "outputs": [ + { + "name": "align_summary", + "type": "txt" + }, + { + "name": "fusions", + "type": "tabular" + }, + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + }, + { + "name": "unmapped", + "type": "bam" + } + ], + "position": { + "left": 1141, + "top": 279 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 2}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"output_unmapped\\\": \\\"False\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": \\\"mm10_genes.gtf\\\", \\\"use_annotations\\\": \\\"indexed\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "2.1.0", + "type": "tool", + "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", + "workflow_outputs": [] + }, + "6": { + "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "id": 6, + "input_connections": { + "alignments": { + "id": 5, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output", + "type": "tabular" + }, + { + "name": "output_summary", + "type": "tabular" + } + ], + "position": { + "left": 1441, + "top": 388 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/mm10_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.4.6.p5", + "type": "tool", + "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", + "workflow_outputs": [] + } + }, + "uuid": "b8caaaab-6755-4be2-9b28-d16c66777751" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNA-seq_single_end_with_TopHat_-_hg19.ga Wed Jul 20 16:58:05 2016 -0400 @@ -0,0 +1,215 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\"refinery_type\": \"analysis\"}", + "format-version": "0.1", + "name": "RNA-seq single end with TopHat - hg19", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 342.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 1, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 455.5, + "top": 319.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "id": 2, + "input_connections": { + "paired_end|fastq_in": { + "id": 1, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Trimmomatic", + "outputs": [ + { + "name": "fastq_out_paired", + "type": "input" + }, + { + "name": "fastq_out_unpaired", + "type": "input" + }, + { + "name": "fastq_out_r1_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r1_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out", + "type": "fastqsanger" + } + ], + "position": { + "left": 826, + "top": 295.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"fastq_in\\\": null, \\\"is_paired_end\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"illuminaclip\": \"{\\\"seed_mismatches\\\": \\\"2\\\", \\\"adapter_fasta\\\": \\\"TruSeq3-SE.fa\\\", \\\"__current_case__\\\": 0, \\\"palindrome_clip_threshold\\\": \\\"30\\\", \\\"do_illuminaclip\\\": \\\"True\\\", \\\"simple_clip_threshold\\\": \\\"10\\\"}\"}", + "tool_version": "0.32.3", + "type": "tool", + "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", + "workflow_outputs": [] + }, + "3": { + "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "id": 3, + "input_connections": { + "singlePaired|input1": { + "id": 2, + "output_name": "fastq_out" + } + }, + "inputs": [], + "label": null, + "name": "TopHat", + "outputs": [ + { + "name": "align_summary", + "type": "txt" + }, + { + "name": "fusions", + "type": "tabular" + }, + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + }, + { + "name": "unmapped", + "type": "bam" + } + ], + "position": { + "left": 1189, + "top": 294.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 2}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"output_unmapped\\\": \\\"False\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": \\\"hg19_genes.gtf\\\", \\\"use_annotations\\\": \\\"indexed\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "2.1.0", + "type": "tool", + "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", + "workflow_outputs": [] + }, + "4": { + "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "id": 4, + "input_connections": { + "alignments": { + "id": 3, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output", + "type": "tabular" + }, + { + "name": "output_summary", + "type": "tabular" + } + ], + "position": { + "left": 1458, + "top": 327.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/hg19_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.4.6.p5", + "type": "tool", + "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", + "workflow_outputs": [] + } + }, + "uuid": "b9ffa9cb-2e92-479d-9f38-37c5bbf3983e" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNA-seq_single_end_with_TopHat_-_mm10.ga Wed Jul 20 16:58:05 2016 -0400 @@ -0,0 +1,215 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\"refinery_type\": \"analysis\"}", + "format-version": "0.1", + "name": "RNA-seq single end with TopHat - mm10", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 200, + "top": 345.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "id": 1, + "input_connections": { + "input_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FASTQ Parallel Groomer", + "outputs": [ + { + "name": "output_file", + "type": "fastqsanger" + } + ], + "position": { + "left": 455.5, + "top": 322.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", + "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", + "tool_version": "0.3.1", + "type": "tool", + "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "id": 2, + "input_connections": { + "paired_end|fastq_in": { + "id": 1, + "output_name": "output_file" + } + }, + "inputs": [], + "label": null, + "name": "Trimmomatic", + "outputs": [ + { + "name": "fastq_out_paired", + "type": "input" + }, + { + "name": "fastq_out_unpaired", + "type": "input" + }, + { + "name": "fastq_out_r1_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_paired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r1_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out_r2_unpaired", + "type": "fastqsanger" + }, + { + "name": "fastq_out", + "type": "fastqsanger" + } + ], + "position": { + "left": 826, + "top": 298.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", + "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"fastq_in\\\": null, \\\"is_paired_end\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"illuminaclip\": \"{\\\"seed_mismatches\\\": \\\"2\\\", \\\"adapter_fasta\\\": \\\"TruSeq3-SE.fa\\\", \\\"__current_case__\\\": 0, \\\"palindrome_clip_threshold\\\": \\\"30\\\", \\\"do_illuminaclip\\\": \\\"True\\\", \\\"simple_clip_threshold\\\": \\\"10\\\"}\"}", + "tool_version": "0.32.3", + "type": "tool", + "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", + "workflow_outputs": [] + }, + "3": { + "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "id": 3, + "input_connections": { + "singlePaired|input1": { + "id": 2, + "output_name": "fastq_out" + } + }, + "inputs": [], + "label": null, + "name": "TopHat", + "outputs": [ + { + "name": "align_summary", + "type": "txt" + }, + { + "name": "fusions", + "type": "tabular" + }, + { + "name": "insertions", + "type": "bed" + }, + { + "name": "deletions", + "type": "bed" + }, + { + "name": "junctions", + "type": "bed" + }, + { + "name": "accepted_hits", + "type": "bam" + }, + { + "name": "unmapped", + "type": "bam" + } + ], + "position": { + "left": 1189, + "top": 297.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", + "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 2}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"output_unmapped\\\": \\\"False\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": \\\"mm10_genes.gtf\\\", \\\"use_annotations\\\": \\\"indexed\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "2.1.0", + "type": "tool", + "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", + "workflow_outputs": [] + }, + "4": { + "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}", + "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "id": 4, + "input_connections": { + "alignments": { + "id": 3, + "output_name": "accepted_hits" + } + }, + "inputs": [], + "label": null, + "name": "featureCounts", + "outputs": [ + { + "name": "output", + "type": "tabular" + }, + { + "name": "output_summary", + "type": "tabular" + } + ], + "position": { + "left": 1458, + "top": 330.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", + "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/mm10_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.4.6.p5", + "type": "tool", + "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", + "workflow_outputs": [] + } + }, + "uuid": "7c5e9095-58ea-4e9a-89a5-5c8521d64c7c" +} \ No newline at end of file