--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_test_data	Tue Aug 01 07:56:34 2017 -0400
@@ -0,0 +1,229 @@
+#/usr/bin/env bash
+
+# humann2
+humann2 \
+    --input 'test-data/input_sequences.fasta' \
+    -o 'humann2_output' \
+    --annotation-gene-index 8 \
+    --taxonomic-profile 'test-data/taxonomic_profile.tabular' \
+    --metaphlan-options="-t rel_ab" \
+    --nucleotide-database 'test-data/' \
+    --protein-database 'test-data/' \
+    --evalue '1' \
+    --search-mode 'uniref50' \
+    --prescreen-threshold '0.01' \
+    --identity-threshold '50' \
+    --translated-subject-coverage-threshold '50' \
+    --translated-query-coverage-threshold '50' \
+    --translated-alignment 'diamond' \
+    --xipe 'off' \
+    --minpath 'on' \
+    --pick-frames 'on' \
+    --gap-fill 'off' \
+    --output-format 'tsv' \
+    --output-max-decimals '10' \
+    --output-basename 'humann2' \
+    --pathways 'metacyc'
+
+humann2 \
+    --input 'test-data/input_sequences.fasta' \
+    -o 'humann2_output' \
+    --annotation-gene-index 8 \
+    --metaphlan-options="-t rel_ab" \
+    --nucleotide-database 'test-data/' \
+    --protein-database 'test-data/' \
+    --evalue '1' \
+    --search-mode 'uniref90' \
+    --prescreen-threshold '0.01' \
+    --identity-threshold '50' \
+    --translated-subject-coverage-threshold '50' \
+    --translated-query-coverage-threshold '50' \
+    --translated-alignment 'rapsearch' \
+    --xipe 'off' \
+    --minpath 'on' \
+    --pick-frames 'on' \
+    --gap-fill 'off' \
+    --output-format 'tsv' \
+    --output-max-decimals '10' \
+    --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' \
+    -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
+    --function 'sum' \
+    --groups 'uniref90_infogo1000' \
+    --ungrouped 'Y' \
+    --protected 'Y'
+
+humann2_regroup_table \
+    --input 'test-data/demo_genefamilies.tsv' \
+    -o 'test-data/regrouped_gene_families_to_ko.tsv' \
+    --function 'mean' \
+    --groups 'uniref90_ko' \
+    --ungrouped 'Y' \
+    --protected 'Y'
+
+humann2_regroup_table \
+    --input 'test-data/demo_genefamilies.tsv' \
+    -o 'test-data/regrouped_gene_families_to_rxn.tsv' \
+    --function 'sum' \
+    --groups 'uniref90_rxn' \
+    --ungrouped 'Y' \
+    --protected 'Y'
+
+# humann2_renorm_table
+humann2_renorm_table \
+    --input 'test-data/demo_pathabundance.tsv' \
+    -o 'test-data/cpm_community_renormalized_pathway_abundance.tsv' \
+    --units 'cpm' \
+    --mode 'community' \
+    --special 'n'
+
+humann2_renorm_table \
+    --input 'test-data/demo_pathabundance.tsv' \
+    -o 'test-data/relab_levelwise_renormalized_pathway_abundance.tsv' \
+    --units 'relab' \
+    --mode 'levelwise' \
+    --special 'y'
+
+# humann2_join_tables
+mkdir join_table_tmp_dir
+cp 'test-data/demo_pathabundance.tsv' join_table_tmp_dir
+cp 'test-data/demo_pathcoverage.tsv' join_table_tmp_dir
+humann2_join_tables \
+    -i 'join_table_tmp_dir' \
+    -o 'test-data/joined_pathway_coverage_abundance.tsv'
+
+# humann2_merge_abundance_tables
+humann2_merge_abundance_tables \
+    --input-genes 'test-data/demo_genefamilies.tsv' \
+    --input-pathways 'test-data/demo_pathabundance.tsv' \
+    -o 'test-data/merged_gene_families_pathways_abundances.tsv' 
+
+# humann2_reduce_table
+humann2_reduce_table \
+    --input 'test-data/demo_genefamilies.tsv' \
+    -o 'test-data/max_reduced_gene_family_abundance.tsv' \
+    --function 'max' \
+    --sort-by 'name'
+
+# 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' \
+    --output 'split_stratified_table'
+
+# humann2_split_table
+mkdir split_table_tmp_dir
+humann2_split_table \
+    --input 'test-data/joined_pathway_coverage_abundance.tsv' \
+    -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