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annotate run_secim_tools_test.sh @ 2:caba07f41453 draft default tip

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"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
author malex
date Thu, 10 Jun 2021 15:41:17 +0000
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2
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
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1 #!/bin/bash
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2
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3 echo "Running anova.py"
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4 # Anova
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5 python anova.py \
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6 --input ./test-data/test_data.tsv \
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7 --design ./test-data/test_design.csv \
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8 --ID rowID \
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9 --group treatment \
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10 --out ./test-data/test_anova_tsv.tsv \
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11 --fig ./test-data/test_anova_fig.pdf \
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12 --fig2 ./test-data/test_anova_fig2.pdf
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13 echo "\n\n"
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15 #------------------------------------------
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17 echo "Running baPlot.py"
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18 # Ba Plot
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19 python baPlot.py \
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20 --input ./test-data/test_data.tsv \
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21 --design ./test-data/test_design.csv \
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22 --ID rowID \
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23 --group treatment \
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24 --ba ./test-data/test_baPlot_ba.pdf \
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25 --flag_dist ./test-data/test_baPlot_flag_dist.pdf \
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26 --flag_sample ./test-data/test_baPlot_flag_sample.tsv \
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27 --flag_feature ./test-datatest_baPlot_flag_feature.tsv
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28 echo "\n\n"
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29
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30 #------------------------------------------
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32 echo "Running clean.py"
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33 # Clean
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34 python clean.py \
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35 --input ./test-data/test_data.tsv \
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36 --design ./test-data/test_design.csv \
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37 --ID rowID \
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38 --wideOut ./test-data/test_clean_wideOut.tsv \
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39 --designOut ./test-data/test_clean_designOut.tsv
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40 echo "\n\n"
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42 #------------------------------------------
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44 echo "Running countDigits.py"
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45 # Count Digits
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46 python countDigits.py \
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47 --input ./test-data/test_data.tsv \
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48 --design ./test-data/test_design.csv \
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49 --ID rowID \
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50 --html_path ./test-data/html-path/ \
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51 --html ./test-data/html-path/html.html \
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52 --flags ./test-data/html-path/flags.tsv \
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53 --noZip \
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54 --group treatment
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55 echo "\n\n"
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56
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57 #------------------------------------------
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58
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59 echo "Running CVflag.py"
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60 # CV Flag
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61 python CVflag.py \
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62 --input ./test-data/test_data.tsv \
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63 --design ./test-data/test_design.csv \
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64 --ID rowID \
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65 --CVplotOutFile ./test-data/test_CVplotOutFile.pdf \
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66 --CVflagOutFile ./test-data/test_CVflagOutFile.pdf \
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67 --group treatment
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68 echo "\n\n"
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69
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70 #------------------------------------------
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71
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72 echo "Running distribution.py"
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73 # Distribution
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74 python distribution.py \
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75 --input ./test-data/test_data.tsv \
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76 --design ./test-data/test_design.csv \
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77 --ID rowID \
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78 --fig ./test-data/test_distribution_fig.pdf \
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79 --fig2 ./test-data/test_distribution_fig2.html \
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80 --group treatment
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81 echo "\n\n"
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82
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83 #------------------------------------------
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84
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85 echo "Running dropFlag.py"
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86 # dropFlag
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87 python dropFlag.py \
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88 --input ./test-data/test_data.tsv \
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89 --design ./test-data/test_design.csv \
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90 --ID rowID \
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91 --group treatment \
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92 --flags ./test-data/test_flag.tsv \
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93 --cutoff .5 \
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94 --wideOut ./test-data/test_dropFlag_wideOut.tsv \
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95 --designOut ./test-data/test_dropFlag_designOut.tsv \
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96 --row
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97 echo "\n\n"
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98
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99 #------------------------------------------
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100
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101 # Hierarchical Cluster
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102 #???
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103
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104 #------------------------------------------
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105
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106 echo "Running log_transform.py"
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107 # Log Transform
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108 python log_transform.py \
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109 --input ./test-data/test_data.tsv \
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110 --design ./test-data/test_design.csv \
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111 --ID rowID \
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112 --log log \
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113 --out ./test-data/test_log_transform_out.tsv
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114 echo "\n\n"
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115
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116 #------------------------------------------
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117
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118 echo "Running mean_standardize.py"
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119 # Mean Standardize
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120 python mean_standardize.py \
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121 --input ./test-data/test_data.tsv \
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122 --design ./test-data/test_design.csv \
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123 --ID rowID \
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124 --group treatment \
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125 --std MEAN \
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126 --out ./test-data/test_mean_standardize_out.tsv
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127 echo "\n\n"
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128
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129 #------------------------------------------
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130
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131 echo "Running mergeFlags.py"
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132 # Merge Flags
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133 python mergeFlags.py \
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134 --input ./test-data/test_flag.tsv \
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135 --output ./test-data/test_mergeFlags_output.tsv
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136 echo "\n\n"
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137
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138 #------------------------------------------
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139
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140 echo "Running onOff.py"
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141 # On/Off
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142 python onOff.py \
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143 --input ./test-data/test_data.tsv \
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144 --design ./test-data/test_design.csv \
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145 --ID rowID \
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146 --output ./test-data/test_onOff_output.tsv \
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147 --group treatment \
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148 --cutoff 30000
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149 echo "\n\n"
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150
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151 #------------------------------------------
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152
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153 echo "Running pypca.py"
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154 # Pypca
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155 python pypca.py \
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156 --input ./test-data/test_data.tsv \
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157 --design ./test-data/test_design.csv \
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158 --ID rowID \
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159 --load_out ./test-data/test_pypca_load_out.tsv \
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160 --score_out ./test-data/test_pypca_score_out.tsv
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161 echo "\n\n"
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162
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163 #------------------------------------------
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164
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165
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166 echo "Running RandomForest.py"
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167 # Random Forest
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168 python RandomForest.py \
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169 --input ./test-data/test_data.tsv \
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170 --design ./test-data/test_design.csv \
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171 --ID rowID \
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172 --group treatment \
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173 --num 1000 \
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174 --out ./test-data/test_RandomForest_out.tsv \
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175 --out2 ./test-data/test_RandomForest_out2.tsv
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176 echo "\n\n"
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177
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178 #------------------------------------------
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179
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180 echo "Running RTflag.py"
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181 # RT Flag
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182 python RTflag.py \
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183 --input ./test-data/test_data.tsv \
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184 --design ./test-data/test_design.csv \
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185 --ID rowID \
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186 --RTplotOutFile ./test-data/test_RTflag_RTplotOutFile.tsv \
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187 --RTflagOutFile ./test-data/test_RTflag_RTplotOutFile.png \
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188 --minutes .2
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189 echo "\n\n"
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190
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191 #------------------------------------------
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192
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193 echo "Running runOrderRegression.py"
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194 # Run Order
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195 python runOrderRegression.py \
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196 --input ./test-data/test_data.tsv \
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197 --design ./test-data/test_design.csv \
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198 --ID rowID \
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199 --group treatment \
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200 --order runOrder \
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201 --fig ./test-data/test_runOrderRegression_fig.pdf \
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202 --table ./test-data/test_runOrderRegression_table.pdf
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203 echo "\n\n"
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204
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205 #------------------------------------------
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206
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207 echo "Running scatterPlot3D.py"
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208 Scatter Plot 3D
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209 python scatterPlot3D.py \
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210 --input ./test-data/test_data.tsv \
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211 --design ./test-data/test_design.csv \
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212 --ID rowID \
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213 --group treatment \
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214 --fig ./test-data/test_scatterPlot3D.png \
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215 --xaxis PC1 \
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216 --yaxis PC2 \
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217 --zaxis PC3
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218 echo "\n\n"
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219
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220 #------------------------------------------
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221
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222 echo "Running scatterPlot.py"
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223 # Scatter Plot
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224 python scatterPlot.py \
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225 --input ./test-data/test_data.tsv \
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226 --design ./test-data/test_design.csv \
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227 --ID rowID \
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228 --group treatment \
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229 --fig ./test-data/test_scatterPlot.png \
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230 --xaxis PC1 \
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231 --yaxis PC2
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232 echo "\n\n"
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233
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234 #------------------------------------------
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235
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236 echo "Running standardizedEuclideanDistance.py"
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237 # Standard Euc Distance
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238 python standardizedEuclideanDistance.py \
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239 --input ./test-data/test_data.tsv \
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240 --design ./test-data/test_design.csv \
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241 --ID rowID \
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242 --group treatment \
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243 --SEDplotOutFile ./test-data/test_standardizedEuclideanDistance_SEDplotOutFile.pdf \
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244 --SEDtoCenter ./test-data/test_standardizedEuclideanDistance_SEDtoCenter.tsv \
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245 --SEDpairwise ./test-data/test_standardizedEuclideanDistance_SEDpairwise.tsv
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246 echo "\n\n"
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247
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248 #------------------------------------------
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249
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250 echo "Running SVM_classifier.py"
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251 # SVM
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252 python SVM_classifier.py \
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253 --train_wide ./test-data/test_data.tsv \
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254 --train_design ./test-data/test_design.csv \
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255 --test_wide ./test-data/test_data.tsv \
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256 --test_design ./test-data/test_design.csv \
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257 --class_column_name treatment \
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258 --ID rowID \
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259 --kernel linear \
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260 --degree 3 \
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261 --C 1 \
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262 --a 0.0 \
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263 --b 0.0 \
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264 --outfile ./test-data/test_SVM_classifier_outfile.tsv \
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265 --accuracy_on_training ./test-data/test_SVM_classifier_accuracy_on_training.tsv
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266 echo "\n\n"
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267