Created
August 17, 2016 16:09
-
-
Save lparsons/22c019a295ede562ee8583e44718170a to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| { | |
| "a_galaxy_workflow": "true", | |
| "annotation": "Tophat2 to align reads using only supplied gene model. htseq-count to count uniquely mapping reads that overlap genes in GFF file (type=\"gene\", id=\"ID\")", | |
| "format-version": "0.1", | |
| "name": "gducker: 2015-10 RNA-Seq", | |
| "steps": { | |
| "0": { | |
| "annotation": "", | |
| "content_id": null, | |
| "id": 0, | |
| "input_connections": {}, | |
| "inputs": [ | |
| { | |
| "description": "", | |
| "name": "Input Dataset Collection" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Input dataset collection", | |
| "outputs": [], | |
| "position": { | |
| "left": 200, | |
| "top": 200 | |
| }, | |
| "tool_errors": null, | |
| "tool_id": null, | |
| "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", | |
| "tool_version": null, | |
| "type": "data_collection_input", | |
| "uuid": "7c9d4f4d-2c18-41fd-bc0f-54f1723d06a1", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "0c733a39-ccc5-48ec-95ca-fd2628039b68" | |
| } | |
| ] | |
| }, | |
| "1": { | |
| "annotation": "GTF suitable for use by Tophat (e.g. iGenomes GTF). The gffread program, distributed with cufflinks, will parse the file in the same way as TopHat and can be useful in determining errors or ambiguities.", | |
| "content_id": null, | |
| "id": 1, | |
| "input_connections": {}, | |
| "inputs": [ | |
| { | |
| "description": "GTF suitable for use by Tophat (e.g. iGenomes GTF). The gffread program, distributed with cufflinks, will parse the file in the same way as TopHat and can be useful in determining errors or ambiguities.", | |
| "name": "Gene Model GTF" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Input dataset", | |
| "outputs": [], | |
| "position": { | |
| "left": 200, | |
| "top": 285 | |
| }, | |
| "tool_errors": null, | |
| "tool_id": null, | |
| "tool_state": "{\"name\": \"Gene Model GTF\"}", | |
| "tool_version": null, | |
| "type": "data_input", | |
| "uuid": "None", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "bef9e6f5-ecb5-469b-932b-c6e1af7b2091" | |
| } | |
| ] | |
| }, | |
| "2": { | |
| "annotation": "Twelve column BED file of the genome annotations, generally obtained from UCSC's table browser.", | |
| "content_id": null, | |
| "id": 2, | |
| "input_connections": {}, | |
| "inputs": [ | |
| { | |
| "description": "Twelve column BED file of the genome annotations, generally obtained from UCSC's table browser.", | |
| "name": "Gene Model BED12" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Input dataset", | |
| "outputs": [], | |
| "position": { | |
| "left": 200, | |
| "top": 370 | |
| }, | |
| "tool_errors": null, | |
| "tool_id": null, | |
| "tool_state": "{\"name\": \"Gene Model BED12\"}", | |
| "tool_version": null, | |
| "type": "data_input", | |
| "uuid": "None", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "e2a3286a-3cc6-47fa-9ef5-ec8e08d9c472" | |
| } | |
| ] | |
| }, | |
| "3": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6", | |
| "id": 3, | |
| "input_connections": { | |
| "input": { | |
| "id": 0, | |
| "output_name": "output" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool Cutadapt", | |
| "name": "input" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Cutadapt", | |
| "outputs": [ | |
| { | |
| "name": "report", | |
| "type": "txt" | |
| }, | |
| { | |
| "name": "output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "paired_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "rest_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "wild_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "too_short_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "too_long_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "untrimmed_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "untrimmed_paired_output", | |
| "type": "input" | |
| }, | |
| { | |
| "name": "info_file", | |
| "type": "input" | |
| } | |
| ], | |
| "position": { | |
| "left": 475, | |
| "top": 200 | |
| }, | |
| "post_job_actions": { | |
| "HideDatasetActioninfo_file": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "info_file" | |
| }, | |
| "HideDatasetActionoutput": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "output" | |
| }, | |
| "HideDatasetActionpaired_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "paired_output" | |
| }, | |
| "HideDatasetActionreport": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "report" | |
| }, | |
| "HideDatasetActionrest_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "rest_output" | |
| }, | |
| "HideDatasetActiontoo_long_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "too_long_output" | |
| }, | |
| "HideDatasetActiontoo_short_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "too_short_output" | |
| }, | |
| "HideDatasetActionuntrimmed_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "untrimmed_output" | |
| }, | |
| "HideDatasetActionuntrimmed_paired_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "untrimmed_paired_output" | |
| }, | |
| "HideDatasetActionwild_output": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "wild_output" | |
| }, | |
| "RenameDatasetActionoutput": { | |
| "action_arguments": { | |
| "newname": "#{input} trimmed fastq" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "output" | |
| }, | |
| "RenameDatasetActionreport": { | |
| "action_arguments": { | |
| "newname": "#{input} cutadapt report" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "report" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6", | |
| "tool_shed_repository": { | |
| "changeset_revision": "01d94df2e32a", | |
| "name": "cutadapt", | |
| "owner": "lparsons", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"count\": \"\\\"1\\\"\", \"error_rate\": \"\\\"0.1\\\"\", \"match_read_wildcards\": \"\\\"false\\\"\", \"paired_end\": \"{\\\"paired_end_boolean\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"output_params\": \"{\\\"output_type\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"overlap\": \"\\\"3\\\"\", \"front_adapters\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"no_indels\": \"\\\"false\\\"\", \"anywhere_adapters\": \"[]\", \"adapters\": \"[{\\\"__index__\\\": 0, \\\"adapter_source\\\": {\\\"adapter\\\": \\\"AGATCGGAAGAG\\\", \\\"adapter_source_list\\\": \\\"prebuilt\\\", \\\"__current_case__\\\": 1}}]\", \"read_modification_params\": \"{\\\"read_modification\\\": \\\"none\\\", \\\"__current_case__\\\": 0}\", \"output_filtering_options\": \"{\\\"output_filtering\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", | |
| "tool_version": "1.6", | |
| "type": "tool", | |
| "uuid": "2bbd890e-aa40-4454-a574-d93f8e6c363f", | |
| "workflow_outputs": [] | |
| }, | |
| "4": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.64", | |
| "id": 4, | |
| "input_connections": { | |
| "input_file": { | |
| "id": 0, | |
| "output_name": "output" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool FastQC", | |
| "name": "contaminants" | |
| }, | |
| { | |
| "description": "runtime parameter for tool FastQC", | |
| "name": "limits" | |
| }, | |
| { | |
| "description": "runtime parameter for tool FastQC", | |
| "name": "input_file" | |
| } | |
| ], | |
| "label": null, | |
| "name": "FastQC", | |
| "outputs": [ | |
| { | |
| "name": "html_file", | |
| "type": "html" | |
| }, | |
| { | |
| "name": "text_file", | |
| "type": "txt" | |
| } | |
| ], | |
| "position": { | |
| "left": 475, | |
| "top": 606 | |
| }, | |
| "post_job_actions": { | |
| "RenameDatasetActionhtml_file": { | |
| "action_arguments": { | |
| "newname": "#{input_file}: FastQC Report" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "html_file" | |
| }, | |
| "RenameDatasetActiontext_file": { | |
| "action_arguments": { | |
| "newname": "#{input_file}: FastQC Data" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "text_file" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.64", | |
| "tool_shed_repository": { | |
| "changeset_revision": "28d39af2dd06", | |
| "name": "fastqc", | |
| "owner": "devteam", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"__page__\": 0, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
| "tool_version": "0.64", | |
| "type": "tool", | |
| "uuid": "4f9f13fe-e122-4734-9c24-58019166edf0", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "html_file", | |
| "uuid": "d1318c71-4252-4f81-a64d-8cbfe189b111" | |
| }, | |
| { | |
| "label": null, | |
| "output_name": "text_file", | |
| "uuid": "4bbeb5c6-7ea7-4102-aa7f-a7b194498537" | |
| } | |
| ] | |
| }, | |
| "5": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9", | |
| "id": 5, | |
| "input_connections": { | |
| "params|own_junctions|gene_model_ann|gene_annotation_model": { | |
| "id": 1, | |
| "output_name": "output" | |
| }, | |
| "singlePaired|input1": { | |
| "id": 3, | |
| "output_name": "output" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool TopHat", | |
| "name": "singlePaired" | |
| } | |
| ], | |
| "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": 803, | |
| "top": 200 | |
| }, | |
| "post_job_actions": { | |
| "HideDatasetActiondeletions": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "deletions" | |
| }, | |
| "HideDatasetActionfusions": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "fusions" | |
| }, | |
| "HideDatasetActioninsertions": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "insertions" | |
| }, | |
| "HideDatasetActionjunctions": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "junctions" | |
| }, | |
| "HideDatasetActionunmapped": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "unmapped" | |
| }, | |
| "RenameDatasetActionaccepted_hits": { | |
| "action_arguments": { | |
| "newname": "#{input1} accepted hits" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "accepted_hits" | |
| }, | |
| "RenameDatasetActionalign_summary": { | |
| "action_arguments": { | |
| "newname": "#{input1} alignment summary" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "align_summary" | |
| }, | |
| "RenameDatasetActiondeletions": { | |
| "action_arguments": { | |
| "newname": "#{input1} deletions" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "deletions" | |
| }, | |
| "RenameDatasetActionfusions": { | |
| "action_arguments": { | |
| "newname": "#{input1} fusions" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "fusions" | |
| }, | |
| "RenameDatasetActioninsertions": { | |
| "action_arguments": { | |
| "newname": "#{input1} insertions" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "insertions" | |
| }, | |
| "RenameDatasetActionjunctions": { | |
| "action_arguments": { | |
| "newname": "#{input1} junctions" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "junctions" | |
| }, | |
| "RenameDatasetActionunmapped": { | |
| "action_arguments": { | |
| "newname": "#{input1} unmapped" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "unmapped" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9", | |
| "tool_shed_repository": { | |
| "changeset_revision": "4eb3c3beb9c7", | |
| "name": "tophat2", | |
| "owner": "devteam", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__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-firststrand\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"use_junctions\\\": \\\"Yes\\\", \\\"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\\\": \\\"GRCh38\\\", \\\"__current_case__\\\": 0}\"}", | |
| "tool_version": "0.9", | |
| "type": "tool", | |
| "uuid": "1bf88402-5679-4ef9-8d3f-3fed8eba940d", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "align_summary", | |
| "uuid": "207db5ed-661f-41c6-8846-d54a9f953efb" | |
| }, | |
| { | |
| "label": null, | |
| "output_name": "accepted_hits", | |
| "uuid": "f26e5d00-a823-4230-8ff8-de8fc977e454" | |
| } | |
| ] | |
| }, | |
| "6": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1", | |
| "id": 6, | |
| "input_connections": { | |
| "gfffile": { | |
| "id": 1, | |
| "output_name": "output" | |
| }, | |
| "samfile": { | |
| "id": 5, | |
| "output_name": "accepted_hits" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool htseq-count", | |
| "name": "samfile" | |
| }, | |
| { | |
| "description": "runtime parameter for tool htseq-count", | |
| "name": "gfffile" | |
| } | |
| ], | |
| "label": null, | |
| "name": "htseq-count", | |
| "outputs": [ | |
| { | |
| "name": "counts", | |
| "type": "tabular" | |
| }, | |
| { | |
| "name": "othercounts", | |
| "type": "tabular" | |
| }, | |
| { | |
| "name": "samoutfile", | |
| "type": "bam" | |
| } | |
| ], | |
| "position": { | |
| "left": 1044, | |
| "top": 200 | |
| }, | |
| "post_job_actions": { | |
| "HideDatasetActioncounts": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "counts" | |
| }, | |
| "HideDatasetActionothercounts": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "othercounts" | |
| }, | |
| "HideDatasetActionsamoutfile": { | |
| "action_arguments": {}, | |
| "action_type": "HideDatasetAction", | |
| "output_name": "samoutfile" | |
| }, | |
| "RenameDatasetActioncounts": { | |
| "action_arguments": { | |
| "newname": "#{samfile}: Gene counts" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "counts" | |
| }, | |
| "RenameDatasetActionothercounts": { | |
| "action_arguments": { | |
| "newname": "#{samfile}: Other counts" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "othercounts" | |
| }, | |
| "RenameDatasetActionsamoutfile": { | |
| "action_arguments": { | |
| "newname": "#{samfile}: htseq-count samfile" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "samoutfile" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1", | |
| "tool_shed_repository": { | |
| "changeset_revision": "a6dcb86af112", | |
| "name": "htseq_count", | |
| "owner": "lparsons", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"featuretype\": \"\\\"exon\\\"\", \"samout_conditional\": \"{\\\"samout\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"idattr\": \"\\\"gene_id\\\"\", \"force_sort\": \"\\\"false\\\"\", \"stranded\": \"\\\"yes\\\"\", \"samfile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"gfffile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"minaqual\": \"\\\"10\\\"\", \"mode\": \"\\\"union\\\"\", \"__rerun_remap_job_id__\": null}", | |
| "tool_version": "0.6.1galaxy1", | |
| "type": "tool", | |
| "uuid": "b64d8184-f553-4ce1-9cee-a06b5dd4d55d", | |
| "workflow_outputs": [] | |
| }, | |
| "7": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.4galaxy1", | |
| "id": 7, | |
| "input_connections": { | |
| "input": { | |
| "id": 5, | |
| "output_name": "accepted_hits" | |
| }, | |
| "refgene": { | |
| "id": 2, | |
| "output_name": "output" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool Read Distribution", | |
| "name": "input" | |
| }, | |
| { | |
| "description": "runtime parameter for tool Read Distribution", | |
| "name": "refgene" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Read Distribution", | |
| "outputs": [ | |
| { | |
| "name": "output", | |
| "type": "txt" | |
| } | |
| ], | |
| "position": { | |
| "left": 1044, | |
| "top": 440 | |
| }, | |
| "post_job_actions": { | |
| "RenameDatasetActionoutput": { | |
| "action_arguments": { | |
| "newname": "#{input}: Read Distribution" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "output" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.4galaxy1", | |
| "tool_shed_repository": { | |
| "changeset_revision": "6b33e31bda10", | |
| "name": "rseqc", | |
| "owner": "nilesh", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"__page__\": 0, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"refgene\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
| "tool_version": "2.4galaxy1", | |
| "type": "tool", | |
| "uuid": "a0b0d45d-1bae-4eed-b467-507305424162", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "9161b302-ae89-41eb-b91c-245dfcc847ed" | |
| } | |
| ] | |
| }, | |
| "8": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.4galaxy1", | |
| "id": 8, | |
| "input_connections": { | |
| "input": { | |
| "id": 5, | |
| "output_name": "accepted_hits" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool BAM/SAM Mapping Stats", | |
| "name": "input" | |
| } | |
| ], | |
| "label": null, | |
| "name": "BAM/SAM Mapping Stats", | |
| "outputs": [ | |
| { | |
| "name": "output", | |
| "type": "txt" | |
| } | |
| ], | |
| "position": { | |
| "left": 1044, | |
| "top": 586 | |
| }, | |
| "post_job_actions": { | |
| "RenameDatasetActionoutput": { | |
| "action_arguments": { | |
| "newname": "#{input}: BAM Mapping Statistics" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "output" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.4galaxy1", | |
| "tool_shed_repository": { | |
| "changeset_revision": "6b33e31bda10", | |
| "name": "rseqc", | |
| "owner": "nilesh", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"mapq\": \"\\\"30\\\"\", \"__page__\": 0}", | |
| "tool_version": "2.4galaxy1", | |
| "type": "tool", | |
| "uuid": "43106464-d8ae-46a0-818c-75f33472a77e", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "09279048-373c-422e-87e7-d4cd61875c9b" | |
| } | |
| ] | |
| }, | |
| "9": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0", | |
| "id": 9, | |
| "input_connections": { | |
| "input": { | |
| "id": 5, | |
| "output_name": "accepted_hits" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool IdxStats", | |
| "name": "input" | |
| } | |
| ], | |
| "label": null, | |
| "name": "IdxStats", | |
| "outputs": [ | |
| { | |
| "name": "output", | |
| "type": "tabular" | |
| } | |
| ], | |
| "position": { | |
| "left": 1044, | |
| "top": 705 | |
| }, | |
| "post_job_actions": { | |
| "RenameDatasetActionoutput": { | |
| "action_arguments": { | |
| "newname": "#{input}: BAM Index Statistics" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "output" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0", | |
| "tool_shed_repository": { | |
| "changeset_revision": "87398ae795c7", | |
| "name": "samtools_idxstats", | |
| "owner": "devteam", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
| "tool_version": "2.0", | |
| "type": "tool", | |
| "uuid": "None", | |
| "workflow_outputs": [ | |
| { | |
| "label": null, | |
| "output_name": "output", | |
| "uuid": "036ccc2b-44d6-4e87-9ae9-15110518096a" | |
| } | |
| ] | |
| }, | |
| "10": { | |
| "annotation": "", | |
| "content_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.4galaxy2", | |
| "id": 10, | |
| "input_connections": { | |
| "inputs": { | |
| "id": 5, | |
| "output_name": "accepted_hits" | |
| }, | |
| "refgene": { | |
| "id": 2, | |
| "output_name": "output" | |
| } | |
| }, | |
| "inputs": [ | |
| { | |
| "description": "runtime parameter for tool Gene Body Converage (BAM)", | |
| "name": "inputs" | |
| }, | |
| { | |
| "description": "runtime parameter for tool Gene Body Converage (BAM)", | |
| "name": "refgene" | |
| } | |
| ], | |
| "label": null, | |
| "name": "Gene Body Converage (BAM)", | |
| "outputs": [ | |
| { | |
| "name": "outputcurvespdf", | |
| "type": "pdf" | |
| }, | |
| { | |
| "name": "outputheatmappdf", | |
| "type": "pdf" | |
| }, | |
| { | |
| "name": "outputr", | |
| "type": "txt" | |
| }, | |
| { | |
| "name": "outputtxt", | |
| "type": "txt" | |
| } | |
| ], | |
| "position": { | |
| "left": 1044, | |
| "top": 824 | |
| }, | |
| "post_job_actions": { | |
| "RenameDatasetActionoutputcurvespdf": { | |
| "action_arguments": { | |
| "newname": "Gene Body Coverage Curves" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "outputcurvespdf" | |
| }, | |
| "RenameDatasetActionoutputheatmappdf": { | |
| "action_arguments": { | |
| "newname": "Gene Body Coverage Heatmap" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "outputheatmappdf" | |
| }, | |
| "RenameDatasetActionoutputr": { | |
| "action_arguments": { | |
| "newname": "Gene Body Coverage R-Script" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "outputr" | |
| }, | |
| "RenameDatasetActionoutputtxt": { | |
| "action_arguments": { | |
| "newname": "Gene Body Coverage Data" | |
| }, | |
| "action_type": "RenameDatasetAction", | |
| "output_name": "outputtxt" | |
| } | |
| }, | |
| "tool_errors": null, | |
| "tool_id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.4galaxy2", | |
| "tool_shed_repository": { | |
| "changeset_revision": "f242ee103277", | |
| "name": "rseqc", | |
| "owner": "nilesh", | |
| "tool_shed": "toolshed.g2.bx.psu.edu" | |
| }, | |
| "tool_state": "{\"__page__\": 0, \"inputs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"minimum_length\": \"\\\"100\\\"\", \"refgene\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
| "tool_version": "2.4galaxy2", | |
| "type": "tool", | |
| "uuid": "2749648b-e67b-49fc-84b7-f9ed146d3b07", | |
| "workflow_outputs": [ | |
| { | |
| "label": "Gene Body Coverage Curves", | |
| "output_name": "outputcurvespdf", | |
| "uuid": "db441240-f617-4b75-bf8c-1e279cdafbf2" | |
| }, | |
| { | |
| "label": "Gene Body Coverage Heatmap", | |
| "output_name": "outputheatmappdf", | |
| "uuid": "932256c0-12b5-4243-9961-9828f7d34dfa" | |
| }, | |
| { | |
| "label": "Gene Body Coverage R-Script", | |
| "output_name": "outputr", | |
| "uuid": "eaa4ffad-34f4-4527-9186-7348e88e9559" | |
| }, | |
| { | |
| "label": "Gene Body Coverage Data", | |
| "output_name": "outputtxt", | |
| "uuid": "5c63d69c-8716-486b-827c-a6bec15025bd" | |
| } | |
| ] | |
| } | |
| }, | |
| "uuid": "8b154d8a-1915-41ce-af7a-0b4325cf86ae" | |
| } |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment