

set -ex



add_alpha_to_mapping_file.py -h
add_qiime_labels.py -h
adjust_seq_orientation.py -h
align_seqs.py -h
alpha_diversity.py -h
alpha_rarefaction.py -h
ampliconnoise.py -h
assign_taxonomy.py -h
beta_diversity.py -h
beta_diversity_through_plots.py -h
beta_significance.py -h
blast_wrapper.py -h
categorized_dist_scatterplot.py -h
check_id_map.py -h
clean_raxml_parsimony_tree.py -h
cluster_quality.py -h
collate_alpha.py -h
compare_3d_plots.py -h
compare_alpha_diversity.py -h
compare_categories.py -h
compare_distance_matrices.py -h
compare_taxa_summaries.py -h
compute_core_microbiome.py -h
conditional_uncovered_probability.py -h
consensus_tree.py -h
convert_fastaqual_fastq.py -h
convert_otu_table_to_unifrac_sample_mapping.py -h
convert_unifrac_sample_mapping_to_otu_table.py -h
core_diversity_analyses.py -h
count_seqs.py -h
demultiplex_fasta.py -h
denoiser_preprocess.py -h
denoiser.py -h
denoiser_worker.py -h
denoise_wrapper.py -h
detrend.py -h
dissimilarity_mtx_stats.py -h
distance_matrix_from_mapping.py -h
estimate_observation_richness.py -h
exclude_seqs_by_blast.py -h
extract_barcodes.py -h
extract_seqs_by_sample_id.py -h
filter_alignment.py -h
filter_distance_matrix.py -h
filter_fasta.py -h
filter_otus_by_sample.py -h
filter_otus_from_otu_table.py -h
filter_samples_from_otu_table.py -h
filter_taxa_from_otu_table.py -h
filter_tree.py -h
fix_arb_fasta.py -h
group_significance.py -h
identify_chimeric_seqs.py -h
identify_missing_files.py -h
identify_paired_differences.py -h
inflate_denoiser_output.py -h
insert_seqs_into_tree.py -h
jackknifed_beta_diversity.py -h
join_paired_ends.py -h
load_remote_mapping_file.py -h
make_2d_plots.py -h
make_3d_plots.py -h
make_bipartite_network.py -h
make_bootstrapped_tree.py -h
make_distance_boxplots.py -h
make_distance_comparison_plots.py -h
make_distance_histograms.py -h
make_fastq.py -h
make_library_id_lists.py -h
make_otu_heatmap_html.py -h
make_otu_heatmap.py -h
make_otu_network.py -h
make_otu_table.py -h
make_per_library_sff.py -h
make_phylogeny.py -h
make_prefs_file.py -h
make_qiime_py_file.py -h
make_rarefaction_plots.py -h
make_tep.py -h
map_reads_to_reference.py -h
merge_mapping_files.py -h
merge_otu_maps.py -h
merge_otu_tables.py -h
multiple_rarefactions_even_depth.py -h
multiple_rarefactions.py -h
neighbor_joining.py -h
nmds.py -h
otu_category_significance.py -h
parallel_align_seqs_pynast.py -h
parallel_alpha_diversity.py -h
parallel_assign_taxonomy_blast.py -h
parallel_assign_taxonomy_rdp.py -h
parallel_assign_taxonomy_uclust.py -h
parallel_beta_diversity.py -h
parallel_blast.py -h
parallel_identify_chimeric_seqs.py -h
parallel_map_reads_to_reference.py -h
parallel_merge_otu_tables.py -h
parallel_multiple_rarefactions.py -h
parallel_pick_otus_blast.py -h
parallel_pick_otus_trie.py -h
parallel_pick_otus_uclust_ref.py -h
parallel_pick_otus_usearch61_ref.py -h
pick_closed_reference_otus.py -h
pick_de_novo_otus.py -h
pick_open_reference_otus.py -h
pick_otus.py -h
pick_rep_set.py -h
plot_rank_abundance_graph.py -h
plot_semivariogram.py -h
plot_taxa_summary.py -h
poller_example.py -h
poller.py -h
principal_coordinates.py -h
print_metadata_stats.py -h
print_qiime_config.py -h
process_iseq.py -h
process_qseq.py -h
process_sff.py -h
quality_scores_plot.py -h
relatedness.py -h
shared_phylotypes.py -h
simsam.py -h
single_rarefaction.py -h
sort_otu_table.py -h
split_fasta_on_sample_ids.py -h
split_libraries_fastq.py -h
split_libraries.py -h
split_otu_table_by_taxonomy.py -h
split_otu_table.py -h
start_parallel_jobs.py -h
start_parallel_jobs_sc.py -h
start_parallel_jobs_torque.py -h
submit_to_mgrast.py -h
subsample_fasta.py -h
summarize_otu_by_cat.py -h
summarize_taxa.py -h
summarize_taxa_through_plots.py -h
supervised_learning.py -h
transform_coordinate_matrices.py -h
tree_compare.py -h
trflp_file_to_otu_table.py -h
trim_sff_primers.py -h
truncate_fasta_qual_files.py -h
truncate_reverse_primer.py -h
unweight_fasta.py -h
upgma_cluster.py -h
validate_demultiplexed_fasta.py -h
validate_mapping_file.py -h
exit 0
