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7
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1 {
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3 "annotation": "This workflow uses SAMTools to call SNPs and INDELs.",
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6 "steps": {
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15 }
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16 ],
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19 "outputs": [],
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23 },
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27 "tool_version": null,
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28 "type": "data_input",
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29 "user_outputs": [],
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30 "uuid": "955f71da-3fad-46c4-a1d9-b0b1cb484569"
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31 },
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32 "1": {
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35 "input_connections": {},
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36 "inputs": [
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37 {
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39 "name": "Reference genome."
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40 }
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41 ],
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42 "label": null,
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43 "name": "Input dataset",
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44 "outputs": [],
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45 "position": {
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48 },
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49 "tool_errors": null,
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52 "tool_version": null,
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53 "type": "data_input",
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54 "user_outputs": [],
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55 "uuid": "7069b8d2-a89a-472a-8e18-b5b8f076de33"
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56 },
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57 "2": {
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58 "annotation": "",
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60 "input_connections": {
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63 "output_name": "output"
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64 }
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65 },
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66 "inputs": [],
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67 "label": null,
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68 "name": "SortSam",
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69 "outputs": [
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70 {
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71 "name": "outFile",
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72 "type": "bam"
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73 }
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75 "position": {
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76 "left": 436.5,
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77 "top": 121
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78 },
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79 "post_job_actions": {},
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80 "tool_errors": null,
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81 "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_SortSam/1.135",
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82 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"coordinate\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
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83 "tool_version": "1.135",
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84 "type": "tool",
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85 "user_outputs": [],
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86 "uuid": "b06955b6-6bba-4aaa-a919-fbb2aba9fdf5"
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87 },
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88 "3": {
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89 "annotation": "",
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90 "id": 3,
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91 "input_connections": {
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96 "reference_source|ref_file": {
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97 "id": 1,
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98 "output_name": "output"
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99 }
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100 },
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101 "inputs": [],
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102 "label": null,
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103 "name": "MPileup",
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104 "outputs": [
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105 {
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106 "name": "output_mpileup",
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107 "type": "pileup"
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108 },
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109 {
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110 "name": "output_log",
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111 "type": "txt"
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112 }
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113 ],
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114 "position": {
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116 "top": 192
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117 },
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118 "post_job_actions": {},
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119 "tool_errors": null,
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120 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
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121 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}",
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122 "tool_version": "0.0.3",
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123 "type": "tool",
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124 "user_outputs": [],
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125 "uuid": "99b58983-e355-4357-b77e-8e29afcdc866"
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126 }
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127 },
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128 "uuid": "6b217aca-887a-4cca-91e4-446a7cc50726"
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129 } |
