--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_secim_tools_test.sh	Thu Jun 10 15:41:17 2021 +0000
@@ -0,0 +1,267 @@
+#!/bin/bash
+
+echo "Running anova.py"
+# Anova
+python anova.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --out ./test-data/test_anova_tsv.tsv \
+    --fig ./test-data/test_anova_fig.pdf \
+    --fig2 ./test-data/test_anova_fig2.pdf
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running baPlot.py"
+# Ba Plot
+python baPlot.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --ba ./test-data/test_baPlot_ba.pdf \
+    --flag_dist ./test-data/test_baPlot_flag_dist.pdf \
+    --flag_sample ./test-data/test_baPlot_flag_sample.tsv \
+    --flag_feature ./test-datatest_baPlot_flag_feature.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running clean.py"
+# Clean
+python clean.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --wideOut ./test-data/test_clean_wideOut.tsv \
+    --designOut ./test-data/test_clean_designOut.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running countDigits.py"
+# Count Digits
+python countDigits.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --html_path ./test-data/html-path/ \
+    --html ./test-data/html-path/html.html \
+    --flags ./test-data/html-path/flags.tsv \
+    --noZip \
+    --group treatment
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running CVflag.py"
+# CV Flag
+python CVflag.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --CVplotOutFile ./test-data/test_CVplotOutFile.pdf \
+    --CVflagOutFile ./test-data/test_CVflagOutFile.pdf \
+    --group treatment
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running distribution.py"
+# Distribution
+python distribution.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --fig ./test-data/test_distribution_fig.pdf \
+    --fig2 ./test-data/test_distribution_fig2.html \
+    --group treatment
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running dropFlag.py"
+# dropFlag
+python dropFlag.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --flags ./test-data/test_flag.tsv \
+    --cutoff .5 \
+    --wideOut ./test-data/test_dropFlag_wideOut.tsv \
+    --designOut ./test-data/test_dropFlag_designOut.tsv \
+    --row
+echo "\n\n"
+
+#------------------------------------------
+
+# Hierarchical Cluster
+#???
+
+#------------------------------------------
+
+echo "Running log_transform.py"
+# Log Transform
+python log_transform.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --log log \
+    --out ./test-data/test_log_transform_out.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running mean_standardize.py"
+# Mean Standardize
+python mean_standardize.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --std MEAN \
+    --out ./test-data/test_mean_standardize_out.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running mergeFlags.py"
+# Merge Flags
+python mergeFlags.py \
+        --input ./test-data/test_flag.tsv \
+        --output ./test-data/test_mergeFlags_output.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running onOff.py"
+# On/Off
+python onOff.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --output ./test-data/test_onOff_output.tsv \
+    --group treatment \
+    --cutoff 30000
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running pypca.py"
+# Pypca
+python pypca.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --load_out ./test-data/test_pypca_load_out.tsv \
+    --score_out ./test-data/test_pypca_score_out.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+
+echo "Running RandomForest.py"
+# Random Forest
+python RandomForest.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --num 1000 \
+    --out ./test-data/test_RandomForest_out.tsv \
+    --out2 ./test-data/test_RandomForest_out2.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running RTflag.py"
+# RT Flag
+python RTflag.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --RTplotOutFile ./test-data/test_RTflag_RTplotOutFile.tsv \
+    --RTflagOutFile ./test-data/test_RTflag_RTplotOutFile.png \
+    --minutes .2
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running runOrderRegression.py"
+# Run Order
+python runOrderRegression.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --order runOrder \
+    --fig ./test-data/test_runOrderRegression_fig.pdf \
+    --table ./test-data/test_runOrderRegression_table.pdf
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running scatterPlot3D.py"
+ Scatter Plot 3D
+python scatterPlot3D.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --fig ./test-data/test_scatterPlot3D.png \
+    --xaxis PC1 \
+    --yaxis PC2 \
+    --zaxis PC3
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running scatterPlot.py"
+# Scatter Plot
+python scatterPlot.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --fig ./test-data/test_scatterPlot.png \
+    --xaxis PC1 \
+    --yaxis PC2
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running standardizedEuclideanDistance.py"
+# Standard Euc Distance
+python standardizedEuclideanDistance.py \
+    --input ./test-data/test_data.tsv \
+    --design ./test-data/test_design.csv \
+    --ID rowID \
+    --group treatment \
+    --SEDplotOutFile ./test-data/test_standardizedEuclideanDistance_SEDplotOutFile.pdf \
+    --SEDtoCenter ./test-data/test_standardizedEuclideanDistance_SEDtoCenter.tsv \
+    --SEDpairwise ./test-data/test_standardizedEuclideanDistance_SEDpairwise.tsv
+echo "\n\n"
+
+#------------------------------------------
+
+echo "Running SVM_classifier.py"
+# SVM
+python SVM_classifier.py \
+    --train_wide ./test-data/test_data.tsv \
+    --train_design ./test-data/test_design.csv \
+    --test_wide ./test-data/test_data.tsv \
+    --test_design ./test-data/test_design.csv \
+    --class_column_name treatment \
+    --ID rowID \
+    --kernel linear \
+    --degree 3 \
+    --C 1 \
+    --a 0.0 \
+    --b 0.0 \
+    --outfile ./test-data/test_SVM_classifier_outfile.tsv \
+    --accuracy_on_training ./test-data/test_SVM_classifier_accuracy_on_training.tsv
+echo "\n\n"
+