annotate Galaxy-Workflow-MMuFF_Human_germline_v1.2.ga @ 2:04e170c09922

Add a workflow for noraml tissue samples.
author Jim Johnson <jj@umn.edu>
date Fri, 12 Apr 2013 07:51:45 -0500
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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2 "a_galaxy_workflow": "true",
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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6 "steps": {
04e170c09922 Add a workflow for noraml tissue samples.
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7 "0": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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8 "annotation": "Human RNA-seq paired reads left mates",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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9 "id": 0,
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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13 "description": "Human RNA-seq paired reads left mates",
04e170c09922 Add a workflow for noraml tissue samples.
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14 "name": "Forward reads fastq"
04e170c09922 Add a workflow for noraml tissue samples.
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15 }
04e170c09922 Add a workflow for noraml tissue samples.
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16 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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17 "name": "Input dataset",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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30 "1": {
04e170c09922 Add a workflow for noraml tissue samples.
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31 "annotation": "Human RNA-seq paired reads right mates",
04e170c09922 Add a workflow for noraml tissue samples.
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32 "id": 1,
04e170c09922 Add a workflow for noraml tissue samples.
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33 "input_connections": {},
04e170c09922 Add a workflow for noraml tissue samples.
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34 "inputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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35 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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36 "description": "Human RNA-seq paired reads right mates",
04e170c09922 Add a workflow for noraml tissue samples.
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37 "name": "Reverse reads fastq"
04e170c09922 Add a workflow for noraml tissue samples.
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38 }
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39 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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40 "name": "Input dataset",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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41 "outputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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50 "type": "data_input",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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52 },
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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58 {
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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61 }
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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64 "outputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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91 "name": "FASTQ Groomer",
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92 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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94 "name": "output_file",
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95 "type": "fastqsanger"
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04e170c09922 Add a workflow for noraml tissue samples.
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117 }
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118 },
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04e170c09922 Add a workflow for noraml tissue samples.
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122 "name": "input_type"
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123 }
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124 ],
04e170c09922 Add a workflow for noraml tissue samples.
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125 "name": "FASTQ Groomer",
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126 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
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127 {
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128 "name": "output_file",
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129 "type": "fastqsanger"
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140 "tool_version": "1.0.4",
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141 "type": "tool",
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142 "user_outputs": []
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143 },
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144 "5": {
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145 "annotation": "Map paired reads to reference genome",
04e170c09922 Add a workflow for noraml tissue samples.
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146 "id": 5,
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147 "input_connections": {
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148 "input1": {
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149 "id": 3,
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150 "output_name": "output_file"
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151 },
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154 "output_name": "output_file"
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155 }
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157 "inputs": [],
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158 "name": "Tophat for Illumina",
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159 "outputs": [
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160 {
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164 {
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167 },
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168 {
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171 },
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172 {
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
173 "name": "accepted_hits",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
174 "type": "bam"
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Jim Johnson <jj@umn.edu>
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diff changeset
175 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 ],
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04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
180 },
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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189 "action_type": "HideDatasetAction",
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diff changeset
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
191 },
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
192 "HideDatasetActionjunctions": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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193 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
194 "action_type": "HideDatasetAction",
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Jim Johnson <jj@umn.edu>
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195 "output_name": "junctions"
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Jim Johnson <jj@umn.edu>
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196 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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197 },
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Jim Johnson <jj@umn.edu>
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diff changeset
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diff changeset
199 "tool_id": "tophat",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
200 "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"80\\\"}\"}",
04e170c09922 Add a workflow for noraml tissue samples.
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parents:
diff changeset
201 "tool_version": "1.5.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
202 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 "user_outputs": []
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Jim Johnson <jj@umn.edu>
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204 },
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parents:
diff changeset
205 "6": {
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
206 "annotation": "Keep only mappings with MAPQ of 255",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
207 "id": 6,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
208 "input_connections": {
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Jim Johnson <jj@umn.edu>
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diff changeset
209 "input1": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
210 "id": 5,
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Jim Johnson <jj@umn.edu>
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diff changeset
211 "output_name": "accepted_hits"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
212 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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213 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 "name": "Filter SAM or BAM",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 "name": "output1",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
219 "type": "sam"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
225 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
226 "post_job_actions": {
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Jim Johnson <jj@umn.edu>
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diff changeset
227 "HideDatasetActionoutput1": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
229 "action_type": "HideDatasetAction",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 "output_name": "output1"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 }
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 },
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Jim Johnson <jj@umn.edu>
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diff changeset
233 "tool_errors": null,
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Jim Johnson <jj@umn.edu>
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diff changeset
234 "tool_id": "samtools_filter",
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
235 "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}",
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parents:
diff changeset
236 "tool_version": "1.1.0",
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Jim Johnson <jj@umn.edu>
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diff changeset
237 "type": "tool",
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diff changeset
238 "user_outputs": []
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 },
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
240 "7": {
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diff changeset
241 "annotation": "",
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
242 "id": 7,
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Jim Johnson <jj@umn.edu>
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diff changeset
243 "input_connections": {
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Jim Johnson <jj@umn.edu>
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diff changeset
244 "input1": {
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Jim Johnson <jj@umn.edu>
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diff changeset
245 "id": 6,
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Jim Johnson <jj@umn.edu>
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diff changeset
246 "output_name": "output1"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 }
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Jim Johnson <jj@umn.edu>
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248 },
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249 "inputs": [],
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diff changeset
250 "name": "flagstat",
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Jim Johnson <jj@umn.edu>
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251 "outputs": [
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diff changeset
252 {
04e170c09922 Add a workflow for noraml tissue samples.
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253 "name": "output1",
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Jim Johnson <jj@umn.edu>
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254 "type": "txt"
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Jim Johnson <jj@umn.edu>
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255 }
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Jim Johnson <jj@umn.edu>
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256 ],
04e170c09922 Add a workflow for noraml tissue samples.
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257 "position": {
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
260 },
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diff changeset
261 "post_job_actions": {},
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Jim Johnson <jj@umn.edu>
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diff changeset
262 "tool_errors": null,
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diff changeset
263 "tool_id": "samtools_flagstat",
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parents:
diff changeset
264 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
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parents:
diff changeset
265 "tool_version": "1.0.0",
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
266 "type": "tool",
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Jim Johnson <jj@umn.edu>
parents:
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267 "user_outputs": []
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parents:
diff changeset
268 },
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269 "8": {
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270 "annotation": "Add Read Group info required by GATK tools",
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parents:
diff changeset
271 "id": 8,
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Jim Johnson <jj@umn.edu>
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diff changeset
272 "input_connections": {
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Jim Johnson <jj@umn.edu>
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diff changeset
273 "inputFile": {
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diff changeset
274 "id": 6,
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Jim Johnson <jj@umn.edu>
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diff changeset
275 "output_name": "output1"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
276 }
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 },
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
278 "inputs": [],
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
279 "name": "Add or Replace Groups",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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280 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
281 {
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
282 "name": "outFile",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
283 "type": "bam"
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Jim Johnson <jj@umn.edu>
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diff changeset
284 }
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Jim Johnson <jj@umn.edu>
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diff changeset
285 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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Jim Johnson <jj@umn.edu>
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diff changeset
289 },
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diff changeset
290 "post_job_actions": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
291 "tool_errors": null,
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Jim Johnson <jj@umn.edu>
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diff changeset
292 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
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parents:
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293 "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}",
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parents:
diff changeset
294 "tool_version": "1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 "type": "tool",
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Jim Johnson <jj@umn.edu>
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diff changeset
296 "user_outputs": []
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Jim Johnson <jj@umn.edu>
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diff changeset
297 },
04e170c09922 Add a workflow for noraml tissue samples.
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parents:
diff changeset
298 "9": {
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Jim Johnson <jj@umn.edu>
parents:
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299 "annotation": "Synchronize paired reads",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300 "id": 9,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 "input_connections": {
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 "input_file": {
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Jim Johnson <jj@umn.edu>
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diff changeset
303 "id": 8,
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Jim Johnson <jj@umn.edu>
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diff changeset
304 "output_name": "outFile"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
305 }
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 "inputs": [],
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 "name": "Paired Read Mate Fixer",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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310 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 "name": "out_file",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
312 "type": "bam"
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Jim Johnson <jj@umn.edu>
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diff changeset
313 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
314 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
318 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
319 "post_job_actions": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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320 "HideDatasetActionout_file": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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321 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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322 "action_type": "HideDatasetAction",
04e170c09922 Add a workflow for noraml tissue samples.
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diff changeset
323 "output_name": "out_file"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
324 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
325 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
326 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
327 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
328 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
329 "tool_version": "1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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330 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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331 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
332 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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333 "10": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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334 "annotation": "Remove duplicate reads",
04e170c09922 Add a workflow for noraml tissue samples.
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335 "id": 10,
04e170c09922 Add a workflow for noraml tissue samples.
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336 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
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337 "input_file": {
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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339 "output_name": "out_file"
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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341 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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342 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
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343 "name": "Mark Duplicate reads",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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344 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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345 {
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Jim Johnson <jj@umn.edu>
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346 "name": "out_file",
04e170c09922 Add a workflow for noraml tissue samples.
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347 "type": "bam"
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04e170c09922 Add a workflow for noraml tissue samples.
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349 {
04e170c09922 Add a workflow for noraml tissue samples.
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350 "name": "html_file",
04e170c09922 Add a workflow for noraml tissue samples.
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351 "type": "html"
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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358 "post_job_actions": {},
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359 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
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360 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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361 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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362 "tool_version": "1.56.0",
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363 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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364 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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365 },
04e170c09922 Add a workflow for noraml tissue samples.
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366 "11": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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367 "annotation": "Reorder BAM for GATK tools",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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368 "id": 11,
04e170c09922 Add a workflow for noraml tissue samples.
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369 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
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370 "inputFile": {
04e170c09922 Add a workflow for noraml tissue samples.
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371 "id": 10,
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372 "output_name": "out_file"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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373 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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374 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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375 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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376 "name": "Reorder SAM/BAM",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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377 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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378 {
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379 "name": "outFile",
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380 "type": "bam"
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381 }
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382 ],
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387 "post_job_actions": {},
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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04e170c09922 Add a workflow for noraml tissue samples.
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391 "tool_version": "1.56.0",
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392 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
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393 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
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394 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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395 "12": {
04e170c09922 Add a workflow for noraml tissue samples.
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396 "annotation": "",
04e170c09922 Add a workflow for noraml tissue samples.
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397 "id": 12,
04e170c09922 Add a workflow for noraml tissue samples.
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398 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
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399 "reference_source|input_bam": {
04e170c09922 Add a workflow for noraml tissue samples.
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400 "id": 11,
04e170c09922 Add a workflow for noraml tissue samples.
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401 "output_name": "outFile"
04e170c09922 Add a workflow for noraml tissue samples.
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402 },
04e170c09922 Add a workflow for noraml tissue samples.
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403 "rod_bind_0|rod_bind_type|input_rod": {
04e170c09922 Add a workflow for noraml tissue samples.
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404 "id": 2,
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405 "output_name": "output"
04e170c09922 Add a workflow for noraml tissue samples.
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406 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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407 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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408 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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409 "name": "Realigner Target Creator",
04e170c09922 Add a workflow for noraml tissue samples.
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410 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
411 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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412 "name": "output_interval",
04e170c09922 Add a workflow for noraml tissue samples.
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413 "type": "gatk_interval"
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414 },
04e170c09922 Add a workflow for noraml tissue samples.
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415 {
04e170c09922 Add a workflow for noraml tissue samples.
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416 "name": "output_log",
04e170c09922 Add a workflow for noraml tissue samples.
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417 "type": "txt"
04e170c09922 Add a workflow for noraml tissue samples.
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418 }
04e170c09922 Add a workflow for noraml tissue samples.
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419 ],
04e170c09922 Add a workflow for noraml tissue samples.
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423 },
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424 "post_job_actions": {
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425 "HideDatasetActionoutput_log": {
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426 "action_arguments": {},
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427 "action_type": "HideDatasetAction",
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428 "output_name": "output_log"
04e170c09922 Add a workflow for noraml tissue samples.
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429 }
04e170c09922 Add a workflow for noraml tissue samples.
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430 },
04e170c09922 Add a workflow for noraml tissue samples.
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431 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
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432 "tool_id": "gatk_realigner_target_creator",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
433 "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
434 "tool_version": "0.0.4",
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435 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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436 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
437 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
438 "13": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
439 "annotation": "Perform local realignments for indels",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
440 "id": 13,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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441 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
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442 "reference_source|input_bam": {
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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444 "output_name": "outFile"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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445 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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446 "target_intervals": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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447 "id": 12,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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448 "output_name": "output_interval"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
449 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
450 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
451 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
452 "name": "Indel Realigner",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
453 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
454 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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455 "name": "output_bam",
04e170c09922 Add a workflow for noraml tissue samples.
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456 "type": "bam"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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457 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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458 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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459 "name": "output_log",
04e170c09922 Add a workflow for noraml tissue samples.
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460 "type": "txt"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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461 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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462 ],
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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466 },
04e170c09922 Add a workflow for noraml tissue samples.
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467 "post_job_actions": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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468 "HideDatasetActionoutput_log": {
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
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471 "output_name": "output_log"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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472 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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473 },
04e170c09922 Add a workflow for noraml tissue samples.
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474 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
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04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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476 "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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477 "tool_version": "0.0.6",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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478 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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479 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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480 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
481 "14": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
482 "annotation": "Check again for duplicate reads and eliminate",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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483 "id": 14,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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484 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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485 "input_file": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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486 "id": 13,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
487 "output_name": "output_bam"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
488 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
489 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
490 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
491 "name": "Mark Duplicate reads",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
492 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
493 {
04e170c09922 Add a workflow for noraml tissue samples.
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parents:
diff changeset
494 "name": "out_file",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
495 "type": "bam"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
496 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
497 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
498 "name": "html_file",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
499 "type": "html"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
500 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
501 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
502 "position": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
503 "left": 3174,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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504 "top": 291
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
505 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
506 "post_job_actions": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
507 "HideDatasetActionhtml_file": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
508 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
509 "action_type": "HideDatasetAction",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
510 "output_name": "html_file"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
511 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
512 "HideDatasetActionout_file": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
513 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
514 "action_type": "HideDatasetAction",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
515 "output_name": "out_file"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
516 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
517 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
518 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
519 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
520 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
521 "tool_version": "1.56.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
522 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
523 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
524 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
525 "15": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
526 "annotation": "Determine base calls at each position",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
527 "id": 15,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
528 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
529 "reference_source|input_bams_0|input_bam": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
530 "id": 14,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
531 "output_name": "out_file"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
532 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
533 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
534 "inputs": [],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
535 "name": "MPileup",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
536 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
537 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
538 "name": "output_mpileup",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
539 "type": "pileup"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
540 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
541 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
542 "name": "output_log",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
543 "type": "txt"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
544 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
545 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
546 "position": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
547 "left": 3554,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
548 "top": 265
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
549 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
550 "post_job_actions": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
551 "HideDatasetActionoutput_log": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
552 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
553 "action_type": "HideDatasetAction",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
554 "output_name": "output_log"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
555 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
556 "HideDatasetActionoutput_mpileup": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
557 "action_arguments": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
558 "action_type": "HideDatasetAction",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
559 "output_name": "output_mpileup"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
560 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
561 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
562 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
563 "tool_id": "samtools_mpileup",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
564 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
565 "tool_version": "0.0.1",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
566 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
567 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
568 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
569 "16": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
570 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nVCF_ID = germline",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
571 "id": 16,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
572 "input_connections": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
573 "input_file": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
574 "id": 15,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
575 "output_name": "output_mpileup"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
576 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
577 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
578 "inputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
579 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
580 "description": "runtime parameter for tool Pileup to VCF",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
581 "name": "min_base_qual"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
582 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
583 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
584 "name": "Pileup to VCF",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
585 "outputs": [
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
586 {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
587 "name": "output_file",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
588 "type": "vcf"
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
589 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
590 ],
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
591 "position": {
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
592 "left": 3937,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
593 "top": 258
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
594 },
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
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diff changeset
595 "post_job_actions": {},
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
596 "tool_errors": null,
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
597 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
598 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"germline\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
599 "tool_version": "2.2",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
600 "type": "tool",
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
601 "user_outputs": []
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
602 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
603 }
04e170c09922 Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
604 }