Mercurial > repos > dereeper > haplotype_analysis_workflow
annotate Galaxy-Workflow-Haplotype_analysis.ga @ 0:f81b8b6a97fb draft
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author | dereeper |
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date | Tue, 14 Aug 2018 08:32:12 -0400 |
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children | bd20187f16c5 |
rev | line source |
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1 { |
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2 "a_galaxy_workflow": "true", |
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3 "annotation": "", |
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4 "format-version": "0.1", |
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5 "name": "Haplotype_analysis", |
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6 "steps": { |
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7 "0": { |
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8 "annotation": "", |
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9 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", |
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10 "errors": null, |
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11 "id": 0, |
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12 "input_connections": {}, |
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13 "inputs": [ |
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14 { |
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15 "description": "runtime parameter for tool VCFtools Filter", |
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16 "name": "input" |
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17 } |
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18 ], |
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19 "label": null, |
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20 "name": "VCFtools Filter", |
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21 "outputs": [ |
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22 { |
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23 "name": "fileout", |
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24 "type": "vcf" |
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25 }, |
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26 { |
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27 "name": "fileout_map", |
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28 "type": "tabular" |
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29 }, |
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30 { |
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31 "name": "filelog", |
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32 "type": "txt" |
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33 } |
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34 ], |
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35 "position": { |
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36 "left": 121.5, |
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37 "top": 247 |
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38 }, |
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39 "post_job_actions": {}, |
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40 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", |
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41 "tool_shed_repository": { |
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42 "changeset_revision": null, |
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43 "name": "vcftools_filter_stats_diversity", |
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44 "owner": "vmarcon", |
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45 "tool_shed": "testtoolshed.g2.bx.psu.edu" |
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46 }, |
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47 "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"3\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"4\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", |
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48 "tool_version": "2.0.0", |
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49 "type": "tool", |
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50 "uuid": "4a63fe7d-03bf-4f8a-b744-acc6c333fd56", |
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51 "workflow_outputs": [] |
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52 }, |
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53 "1": { |
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54 "annotation": "", |
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55 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/beagle/Beagle/1.0.0", |
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56 "errors": null, |
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57 "id": 1, |
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58 "input_connections": { |
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59 "vcf_input": { |
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60 "id": 0, |
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61 "output_name": "fileout" |
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62 } |
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63 }, |
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64 "inputs": [ |
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65 { |
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66 "description": "runtime parameter for tool Beagle", |
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67 "name": "vcf_input" |
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68 } |
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69 ], |
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70 "label": null, |
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71 "name": "Beagle", |
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72 "outputs": [ |
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73 { |
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74 "name": "vcf_ouput", |
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75 "type": "vcf" |
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76 }, |
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77 { |
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78 "name": "log", |
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79 "type": "txt" |
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80 } |
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81 ], |
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82 "position": { |
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83 "left": 343.5, |
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84 "top": 355 |
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85 }, |
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86 "post_job_actions": {}, |
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87 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/beagle/Beagle/1.0.0", |
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88 "tool_shed_repository": { |
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89 "changeset_revision": null, |
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90 "name": "beagle", |
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91 "owner": "vmarcon", |
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92 "tool_shed": "testtoolshed.g2.bx.psu.edu" |
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93 }, |
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94 "tool_state": "{\"phase\": \"\\\"5\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"impute\": \"\\\"5\\\"\", \"vcf_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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95 "tool_version": "1.0.0", |
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96 "type": "tool", |
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97 "uuid": "552bf003-578f-46d1-ac19-19dacad937d2", |
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98 "workflow_outputs": [] |
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99 }, |
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100 "2": { |
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101 "annotation": "", |
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102 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/sniplay/getHaplotypesFromPhasedVCF/2.0.0", |
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103 "errors": null, |
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104 "id": 2, |
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105 "input_connections": { |
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106 "input": { |
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107 "id": 1, |
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108 "output_name": "vcf_ouput" |
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109 } |
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110 }, |
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111 "inputs": [ |
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112 { |
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113 "description": "runtime parameter for tool Get Haplotypes From Phased VCF", |
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114 "name": "input" |
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115 } |
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116 ], |
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117 "label": null, |
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118 "name": "Get Haplotypes From Phased VCF", |
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119 "outputs": [ |
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120 { |
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121 "name": "output_distinct", |
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122 "type": "txt" |
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123 }, |
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124 { |
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125 "name": "output_haplo", |
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126 "type": "fasta" |
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127 }, |
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128 { |
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129 "name": "output_distinct_fasta", |
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130 "type": "fasta" |
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131 } |
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132 ], |
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133 "position": { |
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134 "left": 581, |
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135 "top": 194 |
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136 }, |
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137 "post_job_actions": {}, |
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138 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/sniplay/getHaplotypesFromPhasedVCF/2.0.0", |
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139 "tool_shed_repository": { |
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140 "changeset_revision": null, |
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141 "name": "sniplay", |
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142 "owner": "vmarcon", |
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143 "tool_shed": "testtoolshed.g2.bx.psu.edu" |
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144 }, |
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145 "tool_state": "{\"output_label\": \"\\\"Haplotypes\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", |
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146 "tool_version": "2.0.0", |
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147 "type": "tool", |
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148 "uuid": "4bfbaba7-3fc2-4076-82d6-3212c61fcb91", |
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149 "workflow_outputs": [] |
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150 }, |
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151 "3": { |
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152 "annotation": "", |
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153 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/haplophyle/haplophyle/1.0.0", |
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154 "errors": null, |
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155 "id": 3, |
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156 "input_connections": { |
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157 "input": { |
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158 "id": 2, |
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159 "output_name": "output_distinct_fasta" |
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160 } |
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161 }, |
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162 "inputs": [ |
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163 { |
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164 "description": "runtime parameter for tool Haplophyle", |
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165 "name": "input" |
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166 } |
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167 ], |
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168 "label": null, |
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169 "name": "Haplophyle", |
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170 "outputs": [ |
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171 { |
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172 "name": "fileout", |
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173 "type": "json" |
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174 }, |
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175 { |
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176 "name": "dotfile", |
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177 "type": "txt" |
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178 }, |
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179 { |
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180 "name": "filelog", |
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181 "type": "txt" |
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182 } |
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183 ], |
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184 "position": { |
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185 "left": 856.5, |
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186 "top": 377 |
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187 }, |
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188 "post_job_actions": {}, |
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189 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/haplophyle/haplophyle/1.0.0", |
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190 "tool_shed_repository": { |
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191 "changeset_revision": null, |
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192 "name": "haplophyle", |
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193 "owner": "vmarcon", |
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194 "tool_shed": "testtoolshed.g2.bx.psu.edu" |
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195 }, |
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196 "tool_state": "{\"color\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"false\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", |
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197 "tool_version": "1.0.0", |
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198 "type": "tool", |
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199 "uuid": "31d5583a-740b-46e2-80d8-02d0315ac954", |
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200 "workflow_outputs": [] |
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201 }, |
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202 "4": { |
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203 "annotation": "", |
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204 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/cytoscape/Cytoscape/1.0.0", |
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205 "errors": null, |
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206 "id": 4, |
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207 "input_connections": { |
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208 "input": { |
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209 "id": 3, |
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210 "output_name": "fileout" |
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211 } |
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212 }, |
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213 "inputs": [ |
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214 { |
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215 "description": "runtime parameter for tool Cytoscape", |
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216 "name": "input" |
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217 } |
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218 ], |
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219 "label": null, |
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220 "name": "Cytoscape", |
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221 "outputs": [ |
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222 { |
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223 "name": "cytoscape_html", |
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224 "type": "html" |
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225 }, |
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226 { |
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227 "name": "filelog", |
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228 "type": "txt" |
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229 } |
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230 ], |
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231 "position": { |
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232 "left": 1089, |
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233 "top": 270 |
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234 }, |
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235 "post_job_actions": {}, |
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236 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/cytoscape/Cytoscape/1.0.0", |
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237 "tool_shed_repository": { |
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238 "changeset_revision": null, |
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239 "name": "cytoscape", |
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240 "owner": "vmarcon", |
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241 "tool_shed": "testtoolshed.g2.bx.psu.edu" |
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242 }, |
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243 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", |
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244 "tool_version": "1.0.0", |
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245 "type": "tool", |
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246 "uuid": "8e3d9a5c-09a2-4ef1-acd5-07ca5bb43484", |
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247 "workflow_outputs": [] |
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248 } |
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249 }, |
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250 "tags": [], |
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251 "uuid": "2ce7df85-4151-40cc-b636-a135663b90ee" |
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252 } |