comparison RNA-seq_single_end_with_TopHat_-_hg19.ga @ 1:ba1b76257fa5 draft

Update workflows and add dependency info
author stemcellcommons
date Thu, 21 Jul 2016 11:55:13 -0400
parents cbd6667ca478
children
comparison
equal deleted inserted replaced
0:cbd6667ca478 1:ba1b76257fa5
54 "top": 319.5 54 "top": 319.5
55 }, 55 },
56 "post_job_actions": {}, 56 "post_job_actions": {},
57 "tool_errors": null, 57 "tool_errors": null,
58 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 58 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
59 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 59 "tool_shed_repository": {
60 "changeset_revision": "66ca0d174cf2",
61 "name": "fastq_groomer_parallel",
62 "owner": "kevyin",
63 "tool_shed": "toolshed.g2.bx.psu.edu"
64 },
65 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"__current_case__\\\": 0, \\\"options_type_selector\\\": \\\"basic\\\"}\", \"input_file\": \"null\"}",
60 "tool_version": "0.3.1", 66 "tool_version": "0.3.1",
61 "type": "tool", 67 "type": "tool",
62 "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", 68 "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641",
63 "workflow_outputs": [] 69 "workflow_outputs": []
64 }, 70 },
110 "top": 295.5 116 "top": 295.5
111 }, 117 },
112 "post_job_actions": {}, 118 "post_job_actions": {},
113 "tool_errors": null, 119 "tool_errors": null,
114 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", 120 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
115 "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\\\"}\"}", 121 "tool_shed_repository": {
122 "changeset_revision": "f8a9a5eaca8a",
123 "name": "trimmomatic",
124 "owner": "pjbriggs",
125 "tool_shed": "toolshed.g2.bx.psu.edu"
126 },
127 "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\\\"}\"}",
116 "tool_version": "0.32.3", 128 "tool_version": "0.32.3",
117 "type": "tool", 129 "type": "tool",
118 "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", 130 "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c",
119 "workflow_outputs": [] 131 "workflow_outputs": []
120 }, 132 },
166 "top": 294.5 178 "top": 294.5
167 }, 179 },
168 "post_job_actions": {}, 180 "post_job_actions": {},
169 "tool_errors": null, 181 "tool_errors": null,
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", 182 "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0",
171 "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}\"}", 183 "tool_shed_repository": {
184 "changeset_revision": "015a0cc3c012",
185 "name": "tophat2_with_gene_annotations",
186 "owner": "scottx611x",
187 "tool_shed": "toolshed.g2.bx.psu.edu"
188 },
189 "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\\\", \\\"__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\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\"}",
172 "tool_version": "2.1.0", 190 "tool_version": "2.1.0",
173 "type": "tool", 191 "type": "tool",
174 "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", 192 "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5",
175 "workflow_outputs": [] 193 "workflow_outputs": []
176 }, 194 },
202 "top": 327.5 220 "top": 327.5
203 }, 221 },
204 "post_job_actions": {}, 222 "post_job_actions": {},
205 "tool_errors": null, 223 "tool_errors": null,
206 "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", 224 "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5",
207 "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}\"}", 225 "tool_shed_repository": {
226 "changeset_revision": "e04fbcc4e91a",
227 "name": "featurecounts",
228 "owner": "yhoogstrate",
229 "tool_shed": "toolshed.g2.bx.psu.edu"
230 },
231 "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\": \"{\\\"__current_case__\\\": 0, \\\"parameters\\\": \\\"default\\\"}\"}",
208 "tool_version": "1.4.6.p5", 232 "tool_version": "1.4.6.p5",
209 "type": "tool", 233 "type": "tool",
210 "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", 234 "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd",
211 "workflow_outputs": [] 235 "workflow_outputs": []
212 } 236 }