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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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1:2e7d47c0b027 2:caba07f41453
1 #!/bin/bash
2
3 echo "Running anova.py"
4 # Anova
5 python anova.py \
6 --input ./test-data/test_data.tsv \
7 --design ./test-data/test_design.csv \
8 --ID rowID \
9 --group treatment \
10 --out ./test-data/test_anova_tsv.tsv \
11 --fig ./test-data/test_anova_fig.pdf \
12 --fig2 ./test-data/test_anova_fig2.pdf
13 echo "\n\n"
14
15 #------------------------------------------
16
17 echo "Running baPlot.py"
18 # Ba Plot
19 python baPlot.py \
20 --input ./test-data/test_data.tsv \
21 --design ./test-data/test_design.csv \
22 --ID rowID \
23 --group treatment \
24 --ba ./test-data/test_baPlot_ba.pdf \
25 --flag_dist ./test-data/test_baPlot_flag_dist.pdf \
26 --flag_sample ./test-data/test_baPlot_flag_sample.tsv \
27 --flag_feature ./test-datatest_baPlot_flag_feature.tsv
28 echo "\n\n"
29
30 #------------------------------------------
31
32 echo "Running clean.py"
33 # Clean
34 python clean.py \
35 --input ./test-data/test_data.tsv \
36 --design ./test-data/test_design.csv \
37 --ID rowID \
38 --wideOut ./test-data/test_clean_wideOut.tsv \
39 --designOut ./test-data/test_clean_designOut.tsv
40 echo "\n\n"
41
42 #------------------------------------------
43
44 echo "Running countDigits.py"
45 # Count Digits
46 python countDigits.py \
47 --input ./test-data/test_data.tsv \
48 --design ./test-data/test_design.csv \
49 --ID rowID \
50 --html_path ./test-data/html-path/ \
51 --html ./test-data/html-path/html.html \
52 --flags ./test-data/html-path/flags.tsv \
53 --noZip \
54 --group treatment
55 echo "\n\n"
56
57 #------------------------------------------
58
59 echo "Running CVflag.py"
60 # CV Flag
61 python CVflag.py \
62 --input ./test-data/test_data.tsv \
63 --design ./test-data/test_design.csv \
64 --ID rowID \
65 --CVplotOutFile ./test-data/test_CVplotOutFile.pdf \
66 --CVflagOutFile ./test-data/test_CVflagOutFile.pdf \
67 --group treatment
68 echo "\n\n"
69
70 #------------------------------------------
71
72 echo "Running distribution.py"
73 # Distribution
74 python distribution.py \
75 --input ./test-data/test_data.tsv \
76 --design ./test-data/test_design.csv \
77 --ID rowID \
78 --fig ./test-data/test_distribution_fig.pdf \
79 --fig2 ./test-data/test_distribution_fig2.html \
80 --group treatment
81 echo "\n\n"
82
83 #------------------------------------------
84
85 echo "Running dropFlag.py"
86 # dropFlag
87 python dropFlag.py \
88 --input ./test-data/test_data.tsv \
89 --design ./test-data/test_design.csv \
90 --ID rowID \
91 --group treatment \
92 --flags ./test-data/test_flag.tsv \
93 --cutoff .5 \
94 --wideOut ./test-data/test_dropFlag_wideOut.tsv \
95 --designOut ./test-data/test_dropFlag_designOut.tsv \
96 --row
97 echo "\n\n"
98
99 #------------------------------------------
100
101 # Hierarchical Cluster
102 #???
103
104 #------------------------------------------
105
106 echo "Running log_transform.py"
107 # Log Transform
108 python log_transform.py \
109 --input ./test-data/test_data.tsv \
110 --design ./test-data/test_design.csv \
111 --ID rowID \
112 --log log \
113 --out ./test-data/test_log_transform_out.tsv
114 echo "\n\n"
115
116 #------------------------------------------
117
118 echo "Running mean_standardize.py"
119 # Mean Standardize
120 python mean_standardize.py \
121 --input ./test-data/test_data.tsv \
122 --design ./test-data/test_design.csv \
123 --ID rowID \
124 --group treatment \
125 --std MEAN \
126 --out ./test-data/test_mean_standardize_out.tsv
127 echo "\n\n"
128
129 #------------------------------------------
130
131 echo "Running mergeFlags.py"
132 # Merge Flags
133 python mergeFlags.py \
134 --input ./test-data/test_flag.tsv \
135 --output ./test-data/test_mergeFlags_output.tsv
136 echo "\n\n"
137
138 #------------------------------------------
139
140 echo "Running onOff.py"
141 # On/Off
142 python onOff.py \
143 --input ./test-data/test_data.tsv \
144 --design ./test-data/test_design.csv \
145 --ID rowID \
146 --output ./test-data/test_onOff_output.tsv \
147 --group treatment \
148 --cutoff 30000
149 echo "\n\n"
150
151 #------------------------------------------
152
153 echo "Running pypca.py"
154 # Pypca
155 python pypca.py \
156 --input ./test-data/test_data.tsv \
157 --design ./test-data/test_design.csv \
158 --ID rowID \
159 --load_out ./test-data/test_pypca_load_out.tsv \
160 --score_out ./test-data/test_pypca_score_out.tsv
161 echo "\n\n"
162
163 #------------------------------------------
164
165
166 echo "Running RandomForest.py"
167 # Random Forest
168 python RandomForest.py \
169 --input ./test-data/test_data.tsv \
170 --design ./test-data/test_design.csv \
171 --ID rowID \
172 --group treatment \
173 --num 1000 \
174 --out ./test-data/test_RandomForest_out.tsv \
175 --out2 ./test-data/test_RandomForest_out2.tsv
176 echo "\n\n"
177
178 #------------------------------------------
179
180 echo "Running RTflag.py"
181 # RT Flag
182 python RTflag.py \
183 --input ./test-data/test_data.tsv \
184 --design ./test-data/test_design.csv \
185 --ID rowID \
186 --RTplotOutFile ./test-data/test_RTflag_RTplotOutFile.tsv \
187 --RTflagOutFile ./test-data/test_RTflag_RTplotOutFile.png \
188 --minutes .2
189 echo "\n\n"
190
191 #------------------------------------------
192
193 echo "Running runOrderRegression.py"
194 # Run Order
195 python runOrderRegression.py \
196 --input ./test-data/test_data.tsv \
197 --design ./test-data/test_design.csv \
198 --ID rowID \
199 --group treatment \
200 --order runOrder \
201 --fig ./test-data/test_runOrderRegression_fig.pdf \
202 --table ./test-data/test_runOrderRegression_table.pdf
203 echo "\n\n"
204
205 #------------------------------------------
206
207 echo "Running scatterPlot3D.py"
208 Scatter Plot 3D
209 python scatterPlot3D.py \
210 --input ./test-data/test_data.tsv \
211 --design ./test-data/test_design.csv \
212 --ID rowID \
213 --group treatment \
214 --fig ./test-data/test_scatterPlot3D.png \
215 --xaxis PC1 \
216 --yaxis PC2 \
217 --zaxis PC3
218 echo "\n\n"
219
220 #------------------------------------------
221
222 echo "Running scatterPlot.py"
223 # Scatter Plot
224 python scatterPlot.py \
225 --input ./test-data/test_data.tsv \
226 --design ./test-data/test_design.csv \
227 --ID rowID \
228 --group treatment \
229 --fig ./test-data/test_scatterPlot.png \
230 --xaxis PC1 \
231 --yaxis PC2
232 echo "\n\n"
233
234 #------------------------------------------
235
236 echo "Running standardizedEuclideanDistance.py"
237 # Standard Euc Distance
238 python standardizedEuclideanDistance.py \
239 --input ./test-data/test_data.tsv \
240 --design ./test-data/test_design.csv \
241 --ID rowID \
242 --group treatment \
243 --SEDplotOutFile ./test-data/test_standardizedEuclideanDistance_SEDplotOutFile.pdf \
244 --SEDtoCenter ./test-data/test_standardizedEuclideanDistance_SEDtoCenter.tsv \
245 --SEDpairwise ./test-data/test_standardizedEuclideanDistance_SEDpairwise.tsv
246 echo "\n\n"
247
248 #------------------------------------------
249
250 echo "Running SVM_classifier.py"
251 # SVM
252 python SVM_classifier.py \
253 --train_wide ./test-data/test_data.tsv \
254 --train_design ./test-data/test_design.csv \
255 --test_wide ./test-data/test_data.tsv \
256 --test_design ./test-data/test_design.csv \
257 --class_column_name treatment \
258 --ID rowID \
259 --kernel linear \
260 --degree 3 \
261 --C 1 \
262 --a 0.0 \
263 --b 0.0 \
264 --outfile ./test-data/test_SVM_classifier_outfile.tsv \
265 --accuracy_on_training ./test-data/test_SVM_classifier_accuracy_on_training.tsv
266 echo "\n\n"
267