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.
Latest commit f4cda4b Mar 8, 2015
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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 Delete all the output from the qiime_test_data dir Dec 10, 2013
alpha_rarefaction Delete all the output from the qiime_test_data dir Dec 10, 2013
ampliconnoise Delete all the output from the qiime_test_data dir Dec 10, 2013
assign_taxonomy added script test output Oct 9, 2013
beta_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
beta_diversity_through_plots Delete all the output from the qiime_test_data dir Dec 10, 2013
beta_significance Delete all the output from the qiime_test_data dir Dec 10, 2013
blast_wrapper renaming script_test_data as qiime_test_data Apr 3, 2013
cluster_quality renaming script_test_data as qiime_test_data Apr 3, 2013
collapse_samples MAINT/DOC: renamed script for clarity, and expanded documentation Dec 17, 2014
collate_alpha/alpha_div Delete all the output from the qiime_test_data dir Dec 10, 2013
compare_alpha_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
compare_categories Delete all the output from the qiime_test_data dir Dec 10, 2013
compare_distance_matrices Delete all the output from the qiime_test_data dir Dec 10, 2013
compare_taxa_summaries Delete all the output from the qiime_test_data dir Dec 10, 2013
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 TST: removed test output files Dec 22, 2014
conditional_uncovered_probability Delete all the output from the qiime_test_data dir Dec 10, 2013
consensus_tree/jackknifed_trees Delete all the output from the qiime_test_data dir Dec 10, 2013
convert_fastaqual_fastq Delete all the output from the qiime_test_data dir Dec 10, 2013
core_diversity_analyses Delete all the output from the qiime_test_data dir Dec 10, 2013
count_seqs Delete all the output from the qiime_test_data dir Dec 10, 2013
demultiplex_fasta Delete all the output from the qiime_test_data dir Dec 10, 2013
denoiser_preprocess renaming script_test_data as qiime_test_data Apr 3, 2013
differential_abundance add otu_tables folder to qiime_test_data Jan 5, 2015
dissimilarity_mtx_stats/dists Delete all the output from the qiime_test_data dir Dec 10, 2013
distance_matrix_from_mapping Delete all the output from the qiime_test_data dir Dec 10, 2013
estimate_observation_richness Delete all the output from the qiime_test_data dir Dec 10, 2013
exclude_seqs_by_blast Delete all the output from the qiime_test_data dir Dec 10, 2013
extract_reads_from_interleaved_file Addressing comments Feb 18, 2014
extract_seqs_by_sample_id Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_alignment Remove lanemask requirement from qiime config, store lanemask in qiim… Dec 8, 2014
filter_distance_matrix Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_fasta Update of docs and test data Mar 8, 2015
filter_otus_by_sample Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_otus_from_otu_table Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_samples_from_otu_table DOC: update script usage examples Dec 22, 2014
filter_taxa_from_otu_table Delete all the output from the qiime_test_data dir Dec 10, 2013
filter_tree Delete all the output from the qiime_test_data dir Dec 10, 2013
fix_arb_fasta Delete all the output from the qiime_test_data dir Dec 10, 2013
group_significance Renamed script and modified changelog and test data Dec 10, 2013
identify_chimeric_seqs Delete all the output from the qiime_test_data dir Dec 10, 2013
identify_missing_files/ALIGN_BQ7_ renaming script_test_data as qiime_test_data Apr 3, 2013
identify_paired_differences Delete all the output from the qiime_test_data dir Dec 10, 2013
inflate_denoiser_output Delete all the output from the qiime_test_data dir Dec 10, 2013
jackknifed_beta_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
join_paired_ends Delete all the output from the qiime_test_data dir Dec 10, 2013
make_2d_plots Fixing input test files May 4, 2014
make_bipartite_network Delete all the output from the qiime_test_data dir Dec 10, 2013
make_bootstrapped_tree Delete all the output from the qiime_test_data dir Dec 10, 2013
make_distance_boxplots Delete all the output from the qiime_test_data dir Dec 10, 2013
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 Delete all the output from the qiime_test_data dir Dec 10, 2013
make_otu_table Add the mapping file to qiime_test_data Sep 11, 2014
make_phylogeny Delete all the output from the qiime_test_data dir Dec 10, 2013
make_prefs_file Delete all the output from the qiime_test_data dir Dec 10, 2013
make_rarefaction_plots TST: remove make_rarefaction_plots.py output from qiime_test_data Jan 13, 2015
make_tep renaming script_test_data as qiime_test_data Apr 3, 2013
map_reads_to_reference Delete all the output from the qiime_test_data dir Dec 10, 2013
merge_mapping_files Delete all the output from the qiime_test_data dir Dec 10, 2013
merge_otu_maps Delete all the output from the qiime_test_data dir Dec 10, 2013
merge_otu_tables Delete all the output from the qiime_test_data dir Dec 10, 2013
multiple_extract_barcodes DOC: clarify multiple_extract_barcodes.py script docs Dec 22, 2014
multiple_join_paired_ends DOC: update multiple_join_paired_ends.py script docs Dec 22, 2014
multiple_rarefactions Delete all the output from the qiime_test_data dir Dec 10, 2013
multiple_rarefactions_even_depth Delete all the output from the qiime_test_data dir Dec 10, 2013
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 Delete all the output from the qiime_test_data dir Dec 10, 2013
normalize_table add otu_tables folder Jan 5, 2015
observation_metadata_correlation TST: convert observation_metadata_correlation.py test data to JSON BIOM Jan 13, 2015
parallel_align_seqs_pynast Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_alpha_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_assign_taxonomy_blast Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_assign_taxonomy_rdp Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_assign_taxonomy_uclust Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_beta_diversity Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_blast Delete all the output from the qiime_test_data dir Dec 10, 2013
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 Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_pick_otus_blast Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_pick_otus_sortmerna added script usage directory for sortmerna and condition to raise val… Dec 7, 2014
parallel_pick_otus_trie Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_pick_otus_uclust_ref Delete all the output from the qiime_test_data dir Dec 10, 2013
parallel_pick_otus_usearch61_ref Delete all the output from the qiime_test_data dir Dec 10, 2013
pick_closed_reference_otus resolve issue 1682 Oct 2, 2014
pick_de_novo_otus TST: remove RDP from sumaclust params file Jan 14, 2015
pick_open_reference_otus TST: remove RDP classifier from pick_open_ref params Jan 14, 2015
pick_otus Delete all the output from the qiime_test_data dir Dec 10, 2013
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 Delete all the output from the qiime_test_data dir Dec 10, 2013
plot_taxa_summary Delete all the output from the qiime_test_data dir Dec 10, 2013
poller renaming script_test_data as qiime_test_data Apr 3, 2013
principal_coordinates Delete all the output from the qiime_test_data dir Dec 10, 2013
print_metadata_stats Delete all the output from the qiime_test_data dir Dec 10, 2013
quality_scores_plot Delete all the output from the qiime_test_data dir Dec 10, 2013
relatedness Delete all the output from the qiime_test_data dir Dec 10, 2013
shared_phylotypes Delete all the output from the qiime_test_data dir Dec 10, 2013
simsam Delete all the output from the qiime_test_data dir Dec 10, 2013
single_rarefaction Delete all the output from the qiime_test_data dir Dec 10, 2013
sort_otu_table Delete all the output from the qiime_test_data dir Dec 10, 2013
split_libraries Delete all the output from the qiime_test_data dir Dec 10, 2013
split_libraries_fastq this test file isn't used anymore Feb 21, 2014
split_libraries_lea_seq update Jan 22, 2015
split_otu_table Improvements to split_otu_table.py Aug 20, 2014
split_otu_table_by_taxonomy Delete all the output from the qiime_test_data dir Dec 10, 2013
split_sequence_file_on_sample_ids Rename qiime_test_data dir and add fastq file Sep 18, 2014
start_parallel_jobs renaming script_test_data as qiime_test_data Apr 3, 2013
start_parallel_jobs_sc renaming script_test_data as qiime_test_data Apr 3, 2013
start_parallel_jobs_torque renaming script_test_data as qiime_test_data Apr 3, 2013
subsample_fasta Delete all the output from the qiime_test_data dir Dec 10, 2013
summarize_taxa Delete all the output from the qiime_test_data dir Dec 10, 2013
summarize_taxa_through_plots Delete all the output from the qiime_test_data dir Dec 10, 2013
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 Delete all the output from the qiime_test_data dir Dec 10, 2013
trflp_file_to_otu_table Delete all the output from the qiime_test_data dir Dec 10, 2013
truncate_fasta_qual_files Delete all the output from the qiime_test_data dir Dec 10, 2013
truncate_reverse_primer Delete all the output from the qiime_test_data dir Dec 10, 2013
unweight_fasta Delete all the output from the qiime_test_data dir Dec 10, 2013
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