annotate ngsap-vc/SVDetect.ga @ 3:0d10255b5434 draft default tip

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author scisjnu123
date Thu, 03 Oct 2019 10:42:15 -0400
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3
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "SVDetect workflow.",
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4 "format-version": "0.1",
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5 "name": "SVDetect",
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14 "outputs": [
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36 "tool_version": "1.0.0",
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47 "name": "Import data",
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48 "outputs": [
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49 {
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68 "tool_id": "toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/svdetect_import/1.0.0",
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69 "tool_state": "{\"file_name\": \"\\\"file1\\\"\", \"__rerun_remap_job_id__\": null, \"type\": \"{\\\"file_type\\\": \\\"len\\\", \\\"__current_case__\\\": 1}\", \"file_path\": \"\\\"\\\"\", \"__page__\": 0}",
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70 "tool_version": "1.0.0",
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71 "type": "tool",
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86 "name": "BAM preprocessing",
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87 "outputs": [
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88 {
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107 "tool_id": "toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/svdetect_preprocessing/1.0.0",
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108 "tool_state": "{\"__page__\": 0, \"isizeMin\": \"\\\"0\\\"\", \"newBam\": \"{\\\"__current_case__\\\": 1, \\\"pairNormal\\\": \\\"no\\\"}\", \"isizeMax\": \"\\\"10000\\\"\", \"inputBam\": \"null\", \"__rerun_remap_job_id__\": null, \"nbrePair\": \"\\\"1000000\\\"\", \"readType\": \"\\\"1\\\"\", \"sample_name\": \"\\\"sample\\\"\", \"pairType\": \"\\\"1\\\"\", \"foldPair\": \"\\\"3.0\\\"\"}",
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109 "tool_version": "1.0.0",
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110 "type": "tool",
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129 "name": "Detect clusters of anomalously mapped pairs",
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130 "outputs": [
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131 {
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155 "tool_state": "{\"__page__\": 0, \"sv_type\": \"\\\"all\\\"\", \"getLinks\": \"{\\\"window_size\\\": \\\"3000\\\", \\\"step_length\\\": \\\"250\\\", \\\"splitmate\\\": \\\"True\\\", \\\"__current_case__\\\": 1, \\\"linking\\\": \\\"linking\\\"}\", \"mates_file\": \"null\", \"__rerun_remap_job_id__\": null, \"getFilteredLinks\": \"{\\\"nb_pairs_threshold\\\": \\\"5\\\", \\\"filtering\\\": \\\"filtering\\\", \\\"chromosomes\\\": \\\"\\\", \\\"file_conversion\\\": {\\\"file_conversion_select\\\": \\\"do_not_convert\\\", \\\"__current_case__\\\": 0}, \\\"splitlink\\\": \\\"False\\\", \\\"filter1\\\": {\\\"strand_filtering\\\": \\\"strand\\\", \\\"final_score_threshold\\\": \\\"1.0\\\", \\\"__current_case__\\\": 1, \\\"filter2\\\": {\\\"nb_pairs_order_threshold\\\": \\\"2\\\", \\\"order_filtering\\\": \\\"order\\\", \\\"__current_case__\\\": 1, \\\"filter3\\\": {\\\"indel_sigma_threshold\\\": \\\"3.0\\\", \\\"dup_sigma_threshold\\\": \\\"3.0\\\", \\\"singleton_sigma_threshold\\\": \\\"4.0\\\", \\\"__current_case__\\\": 1, \\\"insert_size_filtering\\\": \\\"insert\\\"}, \\\"mu_length\\\": \\\"3000\\\", \\\"sigma_length\\\": \\\"250\\\"}}, \\\"__current_case__\\\": 1, \\\"links2SV\\\": \\\"True\\\"}\", \"read2_length\": \"\\\"50\\\"\", \"read1_length\": \"\\\"50\\\"\", \"sample_name\": \"\\\"sample\\\"\", \"mates_orientation\": \"\\\"FR\\\"\", \"cmap_file\": \"null\"}",
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156 "tool_version": "1.0.0",
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