Mercurial > repos > ulfschaefer > phephenix
comparison Galaxy-Workflow-Phenix_workflow.ga @ 13:b26e4f861e08 draft
Uploaded
author | ulfschaefer |
---|---|
date | Thu, 16 Jun 2016 11:08:38 -0400 |
parents | a3f15f50a4af |
children | 2e5a83c0f78f |
comparison
equal
deleted
inserted
replaced
12:e252b0b9dd99 | 13:b26e4f861e08 |
---|---|
25 "tool_errors": null, | 25 "tool_errors": null, |
26 "tool_id": null, | 26 "tool_id": null, |
27 "tool_state": "{\"name\": \"Reference fasta\"}", | 27 "tool_state": "{\"name\": \"Reference fasta\"}", |
28 "tool_version": null, | 28 "tool_version": null, |
29 "type": "data_input", | 29 "type": "data_input", |
30 "uuid": "e8f09ff7-1ad7-4798-b4e1-5d28171afb9c", | 30 "uuid": "8d026baa-8283-4463-b8ee-6521e4fb616a", |
31 "workflow_outputs": [] | 31 "workflow_outputs": [] |
32 }, | 32 }, |
33 "1": { | 33 "1": { |
34 "annotation": "", | 34 "annotation": "", |
35 "content_id": null, | 35 "content_id": null, |
51 "tool_errors": null, | 51 "tool_errors": null, |
52 "tool_id": null, | 52 "tool_id": null, |
53 "tool_state": "{\"name\": \"R1 fastq\"}", | 53 "tool_state": "{\"name\": \"R1 fastq\"}", |
54 "tool_version": null, | 54 "tool_version": null, |
55 "type": "data_input", | 55 "type": "data_input", |
56 "uuid": "129fd86e-8b0c-4816-bff0-0ca5916064d7", | 56 "uuid": "d35a85d2-12c5-4397-9484-b1ce0e339779", |
57 "workflow_outputs": [] | 57 "workflow_outputs": [] |
58 }, | 58 }, |
59 "2": { | 59 "2": { |
60 "annotation": "", | 60 "annotation": "", |
61 "content_id": null, | 61 "content_id": null, |
77 "tool_errors": null, | 77 "tool_errors": null, |
78 "tool_id": null, | 78 "tool_id": null, |
79 "tool_state": "{\"name\": \"R2 fastqs\"}", | 79 "tool_state": "{\"name\": \"R2 fastqs\"}", |
80 "tool_version": null, | 80 "tool_version": null, |
81 "type": "data_input", | 81 "type": "data_input", |
82 "uuid": "4d4064d2-6fe8-4758-973f-3b869fdc5432", | 82 "uuid": "d7684e32-fa77-4b38-b686-478e2117a2ae", |
83 "workflow_outputs": [] | 83 "workflow_outputs": [] |
84 }, | 84 }, |
85 "3": { | 85 "3": { |
86 "annotation": "", | 86 "annotation": "", |
87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", | 87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", |
125 "tool_errors": null, | 125 "tool_errors": null, |
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", | 126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", |
127 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | 127 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", |
128 "tool_version": "0.7.12.1", | 128 "tool_version": "0.7.12.1", |
129 "type": "tool", | 129 "type": "tool", |
130 "uuid": "698f08bf-70f5-4fbc-b0b2-d4383bb0f46c", | 130 "uuid": "866b5ac0-33f9-48c5-a5e0-f5f52396f3c9", |
131 "workflow_outputs": [] | 131 "workflow_outputs": [] |
132 }, | 132 }, |
133 "4": { | 133 "4": { |
134 "annotation": "", | 134 "annotation": "", |
135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | 135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", |
169 "tool_errors": null, | 169 "tool_errors": null, |
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | 170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", |
171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", | 171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", |
172 "tool_version": "1.0", | 172 "tool_version": "1.0", |
173 "type": "tool", | 173 "type": "tool", |
174 "uuid": "55618bcb-113c-463d-86a5-07c56f36bd2a", | 174 "uuid": "e1d89cee-dcbf-4973-9310-c0861b5595c1", |
175 "workflow_outputs": [] | 175 "workflow_outputs": [] |
176 }, | 176 }, |
177 "5": { | 177 "5": { |
178 "annotation": "", | 178 "annotation": "", |
179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | 179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", |
210 "output_name": "output" | 210 "output_name": "output" |
211 } | 211 } |
212 }, | 212 }, |
213 "tool_errors": null, | 213 "tool_errors": null, |
214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | 214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", |
215 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"ad_ratio\\\": \\\"0.8\\\", \\\"__current_case__\\\": 2, \\\"snp_filter_type_selector\\\": \\\"ad_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}", | 215 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}", |
216 "tool_version": "1.0", | 216 "tool_version": "1.0", |
217 "type": "tool", | 217 "type": "tool", |
218 "uuid": "9107d008-d037-414d-ad61-715ec3c4b3eb", | 218 "uuid": "5677c0b1-1ef2-43c4-b762-43485541f6ab", |
219 "workflow_outputs": [] | 219 "workflow_outputs": [] |
220 } | 220 } |
221 }, | 221 }, |
222 "uuid": "80e0166f-6275-4dfd-b94d-5ce2fd15d6d8" | 222 "uuid": "602a039a-deb5-45dc-bace-697bb32b974a" |
223 } | 223 } |