Mercurial > repos > wolma > mimodd_workflows
comparison Galaxy-Workflow-MiModD_example_workflow_1.ga @ 1:87bfe31ce878 default tip
workflows for MiModD 0.1.6
author | Wolfgang Maier |
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date | Thu, 04 Jun 2015 18:19:52 +0200 |
parents | 9f64313f2ccb |
children |
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0:9f64313f2ccb | 1:87bfe31ce878 |
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12 { | 12 { |
13 "description": "", | 13 "description": "", |
14 "name": "Input Dataset" | 14 "name": "Input Dataset" |
15 } | 15 } |
16 ], | 16 ], |
17 "label": null, | |
17 "name": "Input dataset", | 18 "name": "Input dataset", |
18 "outputs": [], | 19 "outputs": [], |
19 "position": { | 20 "position": { |
20 "left": 172, | 21 "left": 172, |
21 "top": 176 | 22 "top": 176 |
23 "tool_errors": null, | 24 "tool_errors": null, |
24 "tool_id": null, | 25 "tool_id": null, |
25 "tool_state": "{\"name\": \"Input Dataset\"}", | 26 "tool_state": "{\"name\": \"Input Dataset\"}", |
26 "tool_version": null, | 27 "tool_version": null, |
27 "type": "data_input", | 28 "type": "data_input", |
28 "user_outputs": [] | 29 "user_outputs": [], |
30 "uuid": "None" | |
29 }, | 31 }, |
30 "1": { | 32 "1": { |
31 "annotation": "", | 33 "annotation": "", |
32 "id": 1, | 34 "id": 1, |
33 "input_connections": { | 35 "input_connections": { |
35 "id": 0, | 37 "id": 0, |
36 "output_name": "output" | 38 "output_name": "output" |
37 } | 39 } |
38 }, | 40 }, |
39 "inputs": [], | 41 "inputs": [], |
42 "label": null, | |
40 "name": "SNAP Read Alignment", | 43 "name": "SNAP Read Alignment", |
41 "outputs": [ | 44 "outputs": [ |
42 { | 45 { |
43 "name": "outputfile", | 46 "name": "outputfile", |
44 "type": "bam" | 47 "type": "bam" |
49 "top": 368 | 52 "top": 368 |
50 }, | 53 }, |
51 "post_job_actions": {}, | 54 "post_job_actions": {}, |
52 "tool_errors": null, | 55 "tool_errors": null, |
53 "tool_id": "read_alignment", | 56 "tool_id": "read_alignment", |
54 "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", | 57 "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", |
55 "tool_version": "1.0.0", | 58 "tool_version": "1.0.0", |
56 "type": "tool", | 59 "type": "tool", |
57 "user_outputs": [] | 60 "user_outputs": [], |
61 "uuid": "None" | |
58 }, | 62 }, |
59 "2": { | 63 "2": { |
60 "annotation": "", | 64 "annotation": "", |
61 "id": 2, | 65 "id": 2, |
62 "input_connections": { | 66 "input_connections": { |
68 "id": 0, | 72 "id": 0, |
69 "output_name": "output" | 73 "output_name": "output" |
70 } | 74 } |
71 }, | 75 }, |
72 "inputs": [], | 76 "inputs": [], |
77 "label": null, | |
73 "name": "Variant Calling", | 78 "name": "Variant Calling", |
74 "outputs": [ | 79 "outputs": [ |
75 { | 80 { |
76 "name": "output_vcf", | 81 "name": "output_vcf", |
77 "type": "bcf" | 82 "type": "bcf" |
82 "top": 364 | 87 "top": 364 |
83 }, | 88 }, |
84 "post_job_actions": {}, | 89 "post_job_actions": {}, |
85 "tool_errors": null, | 90 "tool_errors": null, |
86 "tool_id": "variant_calling", | 91 "tool_id": "variant_calling", |
87 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", | 92 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", |
88 "tool_version": "1.0.0", | 93 "tool_version": "1.0.0", |
89 "type": "tool", | 94 "type": "tool", |
90 "user_outputs": [] | 95 "user_outputs": [], |
96 "uuid": "None" | |
91 }, | 97 }, |
92 "3": { | 98 "3": { |
93 "annotation": "", | 99 "annotation": "", |
94 "id": 3, | 100 "id": 3, |
95 "input_connections": { | 101 "input_connections": { |
97 "id": 2, | 103 "id": 2, |
98 "output_name": "output_vcf" | 104 "output_name": "output_vcf" |
99 } | 105 } |
100 }, | 106 }, |
101 "inputs": [], | 107 "inputs": [], |
108 "label": null, | |
102 "name": "Extract Variant Sites", | 109 "name": "Extract Variant Sites", |
103 "outputs": [ | 110 "outputs": [ |
104 { | 111 { |
105 "name": "output_vcf", | 112 "name": "output_vcf", |
106 "type": "vcf" | 113 "type": "vcf" |
114 "tool_errors": null, | 121 "tool_errors": null, |
115 "tool_id": "extract_variants", | 122 "tool_id": "extract_variants", |
116 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", | 123 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", |
117 "tool_version": "1.0.0", | 124 "tool_version": "1.0.0", |
118 "type": "tool", | 125 "type": "tool", |
119 "user_outputs": [] | 126 "user_outputs": [], |
127 "uuid": "None" | |
120 }, | 128 }, |
121 "4": { | 129 "4": { |
122 "annotation": "", | 130 "annotation": "", |
123 "id": 4, | 131 "id": 4, |
124 "input_connections": { | 132 "input_connections": { |
126 "id": 2, | 134 "id": 2, |
127 "output_name": "output_vcf" | 135 "output_name": "output_vcf" |
128 } | 136 } |
129 }, | 137 }, |
130 "inputs": [], | 138 "inputs": [], |
139 "label": null, | |
131 "name": "Coverage Statistics", | 140 "name": "Coverage Statistics", |
132 "outputs": [ | 141 "outputs": [ |
133 { | 142 { |
134 "name": "output_vcf", | 143 "name": "output_vcf", |
135 "type": "tabular" | 144 "type": "tabular" |
143 "tool_errors": null, | 152 "tool_errors": null, |
144 "tool_id": "coverage_stats", | 153 "tool_id": "coverage_stats", |
145 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", | 154 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", |
146 "tool_version": "1.0.0", | 155 "tool_version": "1.0.0", |
147 "type": "tool", | 156 "type": "tool", |
148 "user_outputs": [] | 157 "user_outputs": [], |
158 "uuid": "None" | |
149 }, | 159 }, |
150 "5": { | 160 "5": { |
151 "annotation": "", | 161 "annotation": "", |
152 "id": 5, | 162 "id": 5, |
153 "input_connections": { | 163 "input_connections": { |
159 "id": 1, | 169 "id": 1, |
160 "output_name": "outputfile" | 170 "output_name": "outputfile" |
161 } | 171 } |
162 }, | 172 }, |
163 "inputs": [], | 173 "inputs": [], |
174 "label": null, | |
164 "name": "Deletion Prediction for paired-end data", | 175 "name": "Deletion Prediction for paired-end data", |
165 "outputs": [ | 176 "outputs": [ |
166 { | 177 { |
167 "name": "outputfile", | 178 "name": "outputfile", |
168 "type": "gff" | 179 "type": "gff" |
169 } | 180 } |
170 ], | 181 ], |
171 "position": { | 182 "position": { |
172 "left": 1064, | 183 "left": 1031, |
173 "top": 667 | 184 "top": 666 |
174 }, | 185 }, |
175 "post_job_actions": {}, | 186 "post_job_actions": {}, |
176 "tool_errors": null, | 187 "tool_errors": null, |
177 "tool_id": "deletion_prediction", | 188 "tool_id": "deletion_prediction", |
178 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", | 189 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", |
179 "tool_version": "1.0.0", | 190 "tool_version": "1.0.0", |
180 "type": "tool", | 191 "type": "tool", |
181 "user_outputs": [] | 192 "user_outputs": [], |
193 "uuid": "None" | |
182 } | 194 } |
183 } | 195 }, |
196 "uuid": "cd57b671-cca3-4667-8b2a-1e32d0e86d2c" | |
184 } | 197 } |