Latest commit f4cda4b Mar 8, 2015 @wdwvt1 wdwvt1 Update of docs and test data
filter_fasta.py contained ambiguous documentation for the --sample_id_fp option. Specifically, it was unclear what format the input file for the --sample_id_fp option should be in. This commit does three minor things:
1. Updates the help text for this option so its clear what format is expected.
2. Updates the qiime_test_data/filter_fasta/map.txt so that it conforms to the new documentation and actually exercises the functionality. The current master branch code filters out all sequences.
3. Makes the help options in the script documentation stylistically similar, i.e. same capitalization, punctuation, etc.
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add_alpha_to_mapping_file Delete all the output from the qiime_test_data dir Dec 10, 2013
add_qiime_labels Delete all the output from the qiime_test_data dir Dec 10, 2013
adjust_seq_orientation renaming script_test_data as qiime_test_data Apr 3, 2013
align_seqs Delete all the output from the qiime_test_data dir Dec 10, 2013
alpha_diversity
alpha_rarefaction Delete all the output from the qiime_test_data dir Dec 10, 2013
ampliconnoise
assign_taxonomy
beta_diversity
beta_diversity_through_plots
beta_significance
blast_wrapper
cluster_quality renaming script_test_data as qiime_test_data Apr 3, 2013
collapse_samples
collate_alpha/alpha_div
compare_alpha_diversity
compare_categories Delete all the output from the qiime_test_data dir Dec 10, 2013
compare_distance_matrices
compare_taxa_summaries
compare_trajectories Adding qiime_test_data dir for the compare_trajectories.py script May 28, 2014
compute_core_microbiome Delete all the output from the qiime_test_data dir Dec 10, 2013
compute_taxonomy_ratios
conditional_uncovered_probability
consensus_tree/jackknifed_trees Delete all the output from the qiime_test_data dir Dec 10, 2013
convert_fastaqual_fastq
core_diversity_analyses Delete all the output from the qiime_test_data dir Dec 10, 2013
count_seqs
demultiplex_fasta Delete all the output from the qiime_test_data dir Dec 10, 2013
denoiser_preprocess
differential_abundance
dissimilarity_mtx_stats/dists
distance_matrix_from_mapping Delete all the output from the qiime_test_data dir Dec 10, 2013
estimate_observation_richness
exclude_seqs_by_blast
extract_reads_from_interleaved_file
extract_seqs_by_sample_id Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_alignment
filter_distance_matrix Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_fasta
filter_otus_by_sample
filter_otus_from_otu_table
filter_samples_from_otu_table
filter_taxa_from_otu_table
filter_tree
fix_arb_fasta
group_significance Renamed script and modified changelog and test data Dec 10, 2013
identify_chimeric_seqs
identify_missing_files/ALIGN_BQ7_
identify_paired_differences Delete all the output from the qiime_test_data dir Dec 10, 2013
inflate_denoiser_output
jackknifed_beta_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
join_paired_ends
make_2d_plots Fixing input test files May 4, 2014
make_bipartite_network
make_bootstrapped_tree
make_distance_boxplots
make_distance_comparison_plots Delete all the output from the qiime_test_data dir Dec 10, 2013
make_fastq renaming script_test_data as qiime_test_data Apr 3, 2013
make_otu_heatmap addressing comments Jun 13, 2014
make_otu_network
make_otu_table
make_phylogeny Delete all the output from the qiime_test_data dir Dec 10, 2013
make_prefs_file
make_rarefaction_plots
make_tep
map_reads_to_reference Delete all the output from the qiime_test_data dir Dec 10, 2013
merge_mapping_files
merge_otu_maps
merge_otu_tables
multiple_extract_barcodes
multiple_join_paired_ends
multiple_rarefactions
multiple_rarefactions_even_depth
multiple_split_libraries_fastq DOC: update multiple_split_libraries_fastq.py script docs Dec 23, 2014
neighbor_joining Delete all the output from the qiime_test_data dir Dec 10, 2013
nmds
normalize_table
observation_metadata_correlation TST: convert observation_metadata_correlation.py test data to JSON BIOM Jan 13, 2015
parallel_align_seqs_pynast
parallel_alpha_diversity
parallel_assign_taxonomy_blast Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_assign_taxonomy_rdp
parallel_assign_taxonomy_uclust
parallel_beta_diversity
parallel_blast
parallel_identify_chimeric_seqs Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_map_reads_to_reference Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_merge_otu_tables Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_multiple_rarefactions
parallel_pick_otus_blast
parallel_pick_otus_sortmerna
parallel_pick_otus_trie Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_pick_otus_uclust_ref
parallel_pick_otus_usearch61_ref
pick_closed_reference_otus resolve issue 1682 Oct 2, 2014
pick_de_novo_otus
pick_open_reference_otus TST: remove RDP classifier from pick_open_ref params Jan 14, 2015
pick_otus
pick_rep_set Delete all the output from the qiime_test_data dir Dec 10, 2013
plot_rank_abundance_graph Delete all the output from the qiime_test_data dir Dec 10, 2013
plot_semivariogram
plot_taxa_summary
poller
principal_coordinates
print_metadata_stats Delete all the output from the qiime_test_data dir Dec 10, 2013
quality_scores_plot
relatedness Delete all the output from the qiime_test_data dir Dec 10, 2013
shared_phylotypes
simsam
single_rarefaction Delete all the output from the qiime_test_data dir Dec 10, 2013
sort_otu_table
split_libraries
split_libraries_fastq this test file isn't used anymore Feb 21, 2014
split_libraries_lea_seq
split_otu_table
split_otu_table_by_taxonomy
split_sequence_file_on_sample_ids
start_parallel_jobs
start_parallel_jobs_sc renaming script_test_data as qiime_test_data Apr 3, 2013
start_parallel_jobs_torque
subsample_fasta
summarize_taxa
summarize_taxa_through_plots
supervised_learning Delete all the output from the qiime_test_data dir Dec 10, 2013
transform_coordinate_matrices Fixing tests May 2, 2014
tree_compare
trflp_file_to_otu_table
truncate_fasta_qual_files Delete all the output from the qiime_test_data dir Dec 10, 2013
truncate_reverse_primer
unweight_fasta
upgma_cluster Delete all the output from the qiime_test_data dir Dec 10, 2013
validate_mapping_file Delete all the output from the qiime_test_data dir Dec 10, 2013
__init__.py modified setup.py to install qiime_test_data Apr 3, 2013