annotate Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga @ 1:338a6d724774 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
author galaxyp
date Thu, 16 Mar 2017 08:45:23 -0400
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91 "tool_state": "{\"name\": \"Sample 1 PSM Report\"}",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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92 "tool_version": null,
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galaxyp
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93 "type": "data_input",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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94 "uuid": "2c906b80-b425-4280-9743-4151b15fd3f4",
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galaxyp
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95 "workflow_outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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96 {
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galaxyp
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97 "label": null,
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galaxyp
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98 "output_name": "output",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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99 "uuid": "ba24d136-484f-49c8-964f-982b56b26217"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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100 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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101 ]
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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102 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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103 "3": {
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104 "annotation": "",
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105 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
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galaxyp
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106 "id": 3,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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107 "input_connections": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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108 "tables_0|table": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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109 "id": 0,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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110 "output_name": "output"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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111 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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112 "tables_1|table": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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113 "id": 1,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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114 "output_name": "output"
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galaxyp
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115 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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116 "tables_2|table": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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117 "id": 2,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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118 "output_name": "output"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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119 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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120 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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121 "inputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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122 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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123 "description": "runtime parameter for tool Query Tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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124 "name": "add_to_database"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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125 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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126 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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127 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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128 "name": "Query Tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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129 "outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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130 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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131 "name": "sqlitedb",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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132 "type": "sqlite"
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133 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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134 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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135 "name": "output",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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136 "type": "tabular"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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137 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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138 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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139 "position": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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140 "left": 442,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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141 "top": 230
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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142 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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143 "post_job_actions": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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144 "RenameDatasetActionoutput": {
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145 "action_arguments": {
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146 "newname": "Bering Strait BIOLOGICAL PROCESS"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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147 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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148 "action_type": "RenameDatasetAction",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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149 "output_name": "output"
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150 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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151 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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152 "tool_errors": null,
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153 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
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154 "tool_shed_repository": {
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155 "changeset_revision": "e84d1c3bf4fe",
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156 "name": "query_tabular",
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157 "owner": "jjohnson",
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158 "tool_shed": "toolshed.g2.bx.psu.edu"
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159 },
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160 "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"go\\\", \\\"col_names\\\": \\\"aspect,go_id,description\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_id\\\"}, {\\\"__index__\\\": 1, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"aspect,go_id,description\\\"}]}, \\\"__index__\\\": 0, \\\"input_opts\\\": {\\\"linefilters\\\": []}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 2, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"save_db\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\"\\\\n FROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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161 "tool_version": "2.0.0",
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162 "type": "tool",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
163 "uuid": "8f335601-0ed2-4da1-8d51-3ad443f71400",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
164 "workflow_outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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165 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
166 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
167 "output_name": "output",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
168 "uuid": "e662208f-4587-4b09-9e15-ccc7abb7268a"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
169 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
170 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
171 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
172 "output_name": "sqlitedb",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
173 "uuid": "4b685349-25cb-4459-9950-6207b94bafe6"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
174 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
175 ]
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
176 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
177 "4": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
178 "annotation": "",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
179 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
180 "id": 4,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
181 "input_connections": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
182 "sqlitedb": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
183 "id": 3,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
184 "output_name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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185 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
186 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
187 "inputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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188 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
189 "description": "runtime parameter for tool SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
190 "name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
191 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
192 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
193 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
194 "name": "SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
195 "outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
196 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
197 "name": "query_results",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
198 "type": "tabular"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
199 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
200 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
201 "position": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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diff changeset
202 "left": 874,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
203 "top": 204
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
204 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
205 "post_job_actions": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
206 "RenameDatasetActionquery_results": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
207 "action_arguments": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
208 "newname": "Bering Strait MOLECULAR FUNCTION"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
209 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
210 "action_type": "RenameDatasetAction",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
211 "output_name": "query_results"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
212 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
213 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
214 "tool_errors": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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215 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
216 "tool_shed_repository": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
217 "changeset_revision": "123b9ca5e26a",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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218 "name": "sqlite_to_tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
219 "owner": "jjohnson",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
220 "tool_shed": "toolshed.g2.bx.psu.edu"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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221 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
222 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'molecular_function'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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223 "tool_version": "0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
224 "type": "tool",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
225 "uuid": "ff3593c9-a8eb-4b26-858d-e156de462541",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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226 "workflow_outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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227 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
228 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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229 "output_name": "query_results",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
230 "uuid": "4fd55eff-0f1e-47f2-b4aa-da2ebc91bcda"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
231 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
232 ]
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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233 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
234 "5": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
235 "annotation": "",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
236 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
237 "id": 5,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
238 "input_connections": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
239 "sqlitedb": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
240 "id": 3,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
241 "output_name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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242 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
243 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
244 "inputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
245 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
246 "description": "runtime parameter for tool SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
247 "name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
248 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
249 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
250 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
251 "name": "SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
252 "outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
253 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
254 "name": "query_results",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
255 "type": "tabular"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
256 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
257 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
258 "position": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
259 "left": 876,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
260 "top": 342
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
261 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
262 "post_job_actions": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
263 "RenameDatasetActionquery_results": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
264 "action_arguments": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
265 "newname": "Bering Strait CELLULAR COMPONENT"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
266 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
267 "action_type": "RenameDatasetAction",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
268 "output_name": "query_results"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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269 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
270 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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271 "tool_errors": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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272 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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273 "tool_shed_repository": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
274 "changeset_revision": "123b9ca5e26a",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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275 "name": "sqlite_to_tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
276 "owner": "jjohnson",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
277 "tool_shed": "toolshed.g2.bx.psu.edu"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
278 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
279 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'cellular_component'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
280 "tool_version": "0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
281 "type": "tool",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
282 "uuid": "4aadf296-0c45-43bb-a146-e267c2955233",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
283 "workflow_outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
284 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
285 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
286 "output_name": "query_results",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
287 "uuid": "6042e237-57f6-489e-b8a7-5d32afd39d5e"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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288 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
289 ]
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
290 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
291 "6": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
292 "annotation": "",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
293 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
294 "id": 6,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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diff changeset
295 "input_connections": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
296 "sqlitedb": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
297 "id": 3,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
298 "output_name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
299 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
300 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
301 "inputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
302 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
303 "description": "runtime parameter for tool SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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304 "name": "sqlitedb"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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305 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
306 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
307 "label": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
308 "name": "SQLite to tabular",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
309 "outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
310 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
311 "name": "query_results",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
312 "type": "tabular"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
313 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
314 ],
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
315 "position": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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316 "left": 882,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
317 "top": 458.5
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
318 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
319 "post_job_actions": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
320 "RenameDatasetActionquery_results": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
321 "action_arguments": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
322 "newname": "Bering Strait PEPTIDES and PSMs"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
323 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
324 "action_type": "RenameDatasetAction",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
325 "output_name": "query_results"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
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326 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
327 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
parents:
diff changeset
328 "tool_errors": null,
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
galaxyp
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329 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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330 "tool_shed_repository": {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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331 "changeset_revision": "123b9ca5e26a",
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332 "name": "sqlite_to_tabular",
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333 "owner": "jjohnson",
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334 "tool_shed": "toolshed.g2.bx.psu.edu"
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335 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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336 "tool_state": "{\"sqlquery\": \"\\\"SELECT sequence as \\\\\\\"peptide\\\\\\\", count(id) as \\\\\\\"PSMs\\\\\\\"\\\\nFROM bering_psms\\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95\\\\nGROUP BY sequence\\\\nORDER BY sequence\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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337 "tool_version": "0.0.1",
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338 "type": "tool",
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339 "uuid": "e172020f-dd58-4027-9d6c-94273ec2aee8",
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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340 "workflow_outputs": [
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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341 {
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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342 "label": null,
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343 "output_name": "query_results",
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344 "uuid": "291d94c5-9ff7-44ae-872f-76955c56d6f4"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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345 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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346 ]
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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347 }
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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348 },
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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349 "uuid": "57999e7e-0de6-41e0-87d3-1660414d9896"
338a6d724774 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
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350 }