annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga @ 3:ba15c770fd40 draft

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date Thu, 17 Nov 2016 07:27:04 -0500
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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94 "name": "output_aligned_reads_r",
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95 "type": "fastqsanger"
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96 },
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97 {
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98 "name": "output_unaligned_reads_r",
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99 "type": "fastqsanger"
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100 },
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101 {
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102 "name": "output",
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103 "type": "bam"
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104 },
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105 {
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106 "name": "output_sam",
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107 "type": "sam"
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108 },
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109 {
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110 "name": "mapping_stats",
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112 }
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113 ],
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117 },
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119 "DeleteIntermediatesActionoutput_unaligned_reads_l": {
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122 "output_name": "output_unaligned_reads_l"
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123 },
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124 "HideDatasetActionmapping_stats": {
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125 "action_arguments": {},
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127 "output_name": "mapping_stats"
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128 },
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133 },
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135 "action_arguments": {},
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136 "action_type": "HideDatasetAction",
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137 "output_name": "output_aligned_reads_l"
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138 },
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139 "HideDatasetActionoutput_aligned_reads_r": {
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140 "action_arguments": {},
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141 "action_type": "HideDatasetAction",
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142 "output_name": "output_aligned_reads_r"
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143 },
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144 "HideDatasetActionoutput_sam": {
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145 "action_arguments": {},
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146 "action_type": "HideDatasetAction",
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147 "output_name": "output_sam"
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148 },
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149 "HideDatasetActionoutput_unaligned_reads_l": {
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150 "action_arguments": {},
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151 "action_type": "HideDatasetAction",
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152 "output_name": "output_unaligned_reads_l"
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153 },
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154 "HideDatasetActionoutput_unaligned_reads_r": {
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155 "action_arguments": {},
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156 "action_type": "HideDatasetAction",
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157 "output_name": "output_unaligned_reads_r"
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158 }
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159 },
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160 "tool_errors": null,
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161 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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162 "tool_shed_repository": {
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163 "changeset_revision": "a9d4f71dbfb0",
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164 "name": "bowtie2",
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165 "owner": "devteam",
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166 "tool_shed": "toolshed.g2.bx.psu.edu"
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167 },
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168 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"int_quals\\\": \\\"false\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}",
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169 "tool_version": "2.2.6.2",
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170 "type": "tool",
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171 "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126",
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172 "workflow_outputs": []
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173 },
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174 "3": {
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175 "annotation": "",
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176 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0",
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177 "id": 3,
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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537 },
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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538 "HideDatasetActionfastaOutput": {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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539 "action_arguments": {},
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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540 "action_type": "HideDatasetAction",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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541 "output_name": "fastaOutput"
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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542 },
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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543 "HideDatasetActionun_sequences": {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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544 "action_arguments": {},
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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545 "action_type": "HideDatasetAction",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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546 "output_name": "un_sequences"
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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547 }
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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548 },
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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549 "tool_errors": null,
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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550 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3",
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551 "tool_shed_repository": {
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ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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552 "changeset_revision": "1991c830504a",
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553 "name": "msp_blastparser_and_hits",
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554 "owner": "drosofff",
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555 "tool_shed": "toolshed.g2.bx.psu.edu"
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556 },
48b020a0d2f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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557 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}",
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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558 "tool_version": "2.4.3",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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559 "type": "tool",
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560 "uuid": "30288e33-ff64-4089-9b45-428027744176",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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561 "workflow_outputs": [
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562 {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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563 "label": null,
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564 "output_name": "tabularOutput",
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565 "uuid": "6b25acfc-474c-4852-b196-a14a4cf619e3"
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566 }
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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567 ]
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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568 }
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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569 },
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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570 "uuid": "ea5b1974-4efa-4a30-a29c-4cfa9fd7da83"
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571 }