--- a/generate_test_data	Mon Mar 13 12:38:02 2017 -0400
+++ b/generate_test_data	Tue Aug 01 07:55:06 2017 -0400
@@ -48,6 +48,66 @@
     --output-basename 'humann2' \
     --pathways 'unipathway'
 
+# humann2_associate
+humann2_associate \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-metadatum 'STSite' \
+    --last-metadatum 'STSite' \
+    --focal-type 'categorical' \
+    --fdr '0.2' \
+    --output 'test-data/associate_output.txt'
+
+# humann2_barplot
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort none \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --scaling none \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot1.png
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort sum \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --scaling pseudolog \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot2.pdf
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort metadata \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --exclude-unclassified \
+    --scaling none \
+    --as-genera \
+    --grid \
+    --remove-zeroes \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot3.svg
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --top-strata 12 \
+    --sort sum \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --exclude-unclassified \
+    --scaling normalize \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot4.eps
+
 # humann2_regroup_table
 humann2_regroup_table \
     --input 'test-data/demo_genefamilies.tsv' \
@@ -111,9 +171,34 @@
 
 # humann2_rename_table
 humann2_rename_table \
+    --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
+    --names 'infogo1000' \
+    -o 'test-data/renamed_info1000.tsv'
+    
+humann2_rename_table \
+    --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
+    --custom 'test-data/rename_mapping' \
+    -o 'test-data/renamed_mapping_info1000.tsv'
+
+# humann2_rna_dna_norm
+humann2_rna_dna_norm \
+    --input_dna 'test-data/rna_dna_norm-dna.txt' \
+    --input_rna 'test-data/rna_dna_norm-rna.txt' \
+    --output_basename 'results1' \
+    --method 'laplace'
+
+humann2_rna_dna_norm \
+    --input_dna 'test-data/rna_dna_norm-dna.txt' \
+    --input_rna 'test-data/rna_dna_norm-rna.txt' \
+    --output_basename 'results2' \
+    --method 'witten_bell' \
+    --log_transform \
+    --log_base '2'
+
+# humann2_split_stratified_table
+humann2_split_stratified_table \
     --input 'test-data/demo_genefamilies.tsv' \
-    -o 'test-data/renamed_genefamilies.tsv' \
-    --names 'metacyc-pwy'
+    --output 'split_stratified_table'
 
 # humann2_split_table
 mkdir split_table_tmp_dir
@@ -122,3 +207,23 @@
     -o 'split_table_tmp_dir'
 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'
+
+# humann2_strain_profiler
+humann2_strain_profiler \
+    --input 'test-data/strain_profiler-input.txt' \
+    --critical_mean '1' \
+    --critical_count '2' \
+    --pinterval '1e-10' '1' \
+    --critical_samples '2'
+
+# humann2_unpack_pathways
+humann2_unpack_pathways \
+    --input-genes 'test-data/demo_genefamilies.tsv' \
+    --input-pathways 'test-data/demo_pathabundance.tsv' \
+    --output unpack1
+
+humann2_unpack_pathways \
+    --input-genes 'test-data/demo_genefamilies.tsv' \
+    --input-pathways 'test-data/demo_pathabundance.tsv' \
+    --remove-taxonomy \
+    --output unpack2