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config_file.txt
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config_file.txt
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AutoQiime
add_qiime_labels.py
add_taxa.py
adjust_seq_orientation.py
align_seqs.py blast_db
alpha_diversity.py show_metrics
alpha_rarefaction.py force,print_only
ampliconnoise.py force,print_only
assign_taxonomy.py blast_db
beta_diversity.py show_metrics
beta_diversity_through_plots.py force,print_only
beta_significance.py
blast_wrapper.py
categorized_dist_scatterplot.py
clean_raxml_parsimony_tree.py
cluster_quality.py metric
collate_alpha.py
compare_3d_plots.py
compare_alpha_diversity.py
compare_categories.py
compare_distance_matrices.py
conditional_uncovered_probability.py show_metrics
consensus_tree.py
convert_fastaqual_to_fastq.py
convert_otu_table_to_unifrac_sample_mapping.py
convert_unifrac_sample_mapping_to_otu_table.py
core_qiime_analyses.py force
count_seqs.py
check_id_map.py verbose
denoise_wrapper.py force_overwrite
dissimilarity_mtx_stats.py
distance_matrix_from_mapping.py
#exclude_seqs_by_blast.py -> No se puede integrar en Galaxy porque no se le puede indicar el output (only basename)
extract_seqs_by_sample_id.py
filter_alignment.py
filter_distance_matrix.py
filter_fasta.py
filter_otus_by_sample.py
filter_otus_from_otu_table.py
filter_samples_from_otu_table.py
filter_tree.py
#fix_arb_fasta.py -> que hace exactamente?
identify_chimeric_seqs.py blast_db
#identify_missing_files.py -> necesario en Galaxy?
inflate_denoiser_output.py
insert_seqs_into_tree.py
jackknifed_beta_diversity.py
make_2d_plots.py
make_3d_plots.py
# make_bootstrapped_tree.py -> pone .pdf al final del output_fp si no lo lleva
make_distance_boxplots.py
make_distance_comparison_plots.py
make_distance_histograms.py monte_carlo
make_fastq.py
make_library_id_lists.py debug
make_otu_heatmap_html.py
make_otu_heatmap.py
make_otu_network.py
make_otu_table.py
make_per_library_sff.py
make_phylogeny.py
make_prefs_file.py
make_rarefaction_plots.py webpage
# make_tep.py -> absolute path
merge_mapping_files.py
merge_otu_maps.py
merge_otu_tables.py
multiple_rarefactions_even_depth.py
multiple_rarefactions.py
neighbor_joining.py
nmds.py
otu_category_significance.py
per_library_stats.py
pick_otus.py blast_db
pick_otus_through_otu_table.py
pick_reference_otus_through_otu_table.py
pick_rep_set.py
pick_subsampled_reference_otus_through_otu_table.py force
plot_rank_abundance_graph.py
plot_semivariogram.py
plot_taxa_summary.py
principal_coordinates.py
print_qiime_config.py
# process_iseq.py
process_qseq.py
process_sff.py
quality_scores_plot.py verbose
relatedness.py
shared_phylotypes.py
simsam.py
single_rarefaction.py lineages_included
sort_otu_table.py
split_fasta_on_sample_ids.py
split_libraries_fastq.py last_bad_quality_char
split_libraries.py remove_unassigned
split_otu_table_by_taxonomy.py
split_otu_table.py
submit_to_mgrast.py
subsample_fasta.py
summarize_otu_by_cat.py
summarize_taxa.py relative_abundance
summarize_taxa_through_plots.py force,print_only
supervised_learning.py force
transform_coordinate_matrices.py
tree_compare.py
trflp_file_to_otu_table.py
trim_sff_primers.py
truncate_fasta_qual_files.py
truncate_reverse_primer.py
unweight_fasta.py
upgma_cluster.py
validate_demultiplexed_fasta.py