-
--annotate
-
--annotate_points
-
--color_by COLOR_BY
-
--figsize FIGSIZE FIGSIZE
-
--font_size FONT_SIZE
-
--ggplot2_style
-
--label_padding LABEL_PADDING
-
--output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN
-
--p1 P1
-
--p2 P2
-
--pc_order PC_ORDER
-
--plot_title PLOT_TITLE
-
--save_calculations SAVE_CALCULATIONS
-
--save_lda_input SAVE_LDA_INPUT
-
--scale_by SCALE_BY
-
--scaling_factor SCALING_FACTOR
-
--show_available_metrics
-
--show_significance
-
--stabilize_variance
-
--x_limits X_LIMITS X_LIMITS
-
--y_limits Y_LIMITS Y_LIMITS
-
--z_angles Z_ANGLES Z_ANGLES
-
--z_limits Z_LIMITS Z_LIMITS
-
-a {MRA,NMRA,raw}, --analysis_metric {MRA,NMRA,raw}
-
-b GROUP_BY, --group_by GROUP_BY
-
-c CATEGORY, --category CATEGORY
-
-c COLOR_BY, --color_by COLOR_BY
-
-c COLORS, --colors COLORS
-
-c MAP_CATEGORIES, --map_categories MAP_CATEGORIES
-
-c MAP_CATEGORY, --map_category MAP_CATEGORY
-
-d DIVERSITY [DIVERSITY ...], --diversity DIVERSITY [DIVERSITY ...]
-
-d {2,3}, --dimensions {2,3}
-
-dm DIST_MATRIX_FILE, --dist_matrix_file DIST_MATRIX_FILE
-
-e OUTPUT_TRE, --output_tre OUTPUT_TRE
-
-fo FILTER_OTUIDS_FNH, --filter_otuids_fnh FILTER_OTUIDS_FNH
-
-fp FIL_PCT, --fil_pct FIL_PCT
-
-g GROUP_BY [GROUP_BY ...], --group_by GROUP_BY [GROUP_BY ...]
-
-g GROUP_BY, --group_by GROUP_BY
-
-go GEXF_OUT, --gexf_out GEXF_OUT
-
-h, --help
- command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25]
-
-i ASSIGNED_TAXONOMY_FN, --assigned_taxonomy_fn ASSIGNED_TAXONOMY_FN
-
-i BIOM_FP, --biom_fp BIOM_FP
-
-i COORD_FP, --coord_fp COORD_FP
-
-i INPUT_ASSIGNED_TAXONOMY, --input_assigned_taxonomy INPUT_ASSIGNED_TAXONOMY
-
-i INPUT_BIOM_FP, --input_biom_fp INPUT_BIOM_FP
-
-i INPUT_FASTA_FN, --input_fasta_fn INPUT_FASTA_FN
-
-i INPUT_FNA [INPUT_FNA ...], --input_fna INPUT_FNA [INPUT_FNA ...]
-
-i OTU_ID_FP, --otu_id_fp OTU_ID_FP
-
-i OTU_MAP, --otu_map OTU_MAP
-
-i OTU_TABLE, --otu_table OTU_TABLE
-
-i REP_SET_FP, --rep_set_fp REP_SET_FP
-
-i SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN
-
-ids OTU_IDS_FP, --otu_ids_fp OTU_IDS_FP
|
-
-k SAMPLES_TO_KEEP_FP, --samples_to_keep_fp SAMPLES_TO_KEEP_FP
-
-L {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}
-
-l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}
-
-m MAP_FILE, --map_file MAP_FILE
-
-m MAP_FP, --map_fp MAP_FP
-
-m MAPPING, --mapping MAPPING
-
-m MAPPING_FN, --mapping_fn MAPPING_FN
-
-n JOB_NAME, --job_name JOB_NAME
-
-n NON_UNIQUE_OTU_MATRIX, --non_unique_otu_matrix NON_UNIQUE_OTU_MATRIX
-
-n NON_UNIQUE_OUTPUT_FILE, --non_unique_output_file NON_UNIQUE_OUTPUT_FILE
-
-n NUM_OUTPUT_FILES, --num_output_files NUM_OUTPUT_FILES
-
-o ASSIGNED_TAXONOMY_FP, --assigned_taxonomy_fp ASSIGNED_TAXONOMY_FP
-
-o CONDENSED_SEQS_OTUS_FILE, --condensed_seqs_otus_file CONDENSED_SEQS_OTUS_FILE
-
-o OUT_DIR, --out_dir OUT_DIR
-
-o OUT_FP, --out_fp OUT_FP
-
-o OUTPUT_BIOM_FP, --output_biom_fp OUTPUT_BIOM_FP
-
-o OUTPUT_CSV_FP, --output_csv_fp OUTPUT_CSV_FP
-
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
-
-o OUTPUT_FILTERED_REP_SET_FN, --output_filtered_rep_set_fn OUTPUT_FILTERED_REP_SET_FN
-
-o OUTPUT_FN, --output_fn OUTPUT_FN
-
-o OUTPUT_FP, --output_fp OUTPUT_FP
-
-o OUTPUT_ITOL_TABLE, --output_itol_table OUTPUT_ITOL_TABLE
-
-o OUTPUT_OTU_MAP_FP, --output_otu_map_fp OUTPUT_OTU_MAP_FP
-
-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
-
-o OUTPUT_PRUNED_OTUS_FN, --output_pruned_otus_fn OUTPUT_PRUNED_OTUS_FN
-
-o REPSET_OUT_FP, --repset_out_fp REPSET_OUT_FP
-
-od OUTPUT_DIR, --output_dir OUTPUT_DIR
-
-ot OTU_TABLE, --otu_table OTU_TABLE
-
-p IMAGE_TYPE, --image_type IMAGE_TYPE
-
-p PERCENT_OF_SAMPLES, --percent_of_samples PERCENT_OF_SAMPLES
-
-p PREFIX, --prefix PREFIX
-
-p PRUNED_OUTPUT_FILE, --pruned_output_file PRUNED_OUTPUT_FILE
-
-pc PCOA_FP, --pcoa_fp PCOA_FP
-
-q QUALITY_FN, --quality_fn QUALITY_FN
-
-r REP_SET_FN, --rep_set_fn REP_SET_FN
-
-r REPSET_FP, --repset_fp REPSET_FP
-
-r REVERSE, --reverse REVERSE
-
-s PERCENT_OF_SEQUENCES, --percent_of_sequences PERCENT_OF_SEQUENCES
-
-s POINT_SIZE, --point_size POINT_SIZE
-
-s SAVE_AS, --save_as SAVE_AS
-
-s SEQS_OTUS, --seqs_otus SEQS_OTUS
-
-s SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN
-
-t ID_TO_TAXONOMY_FN, --id_to_taxonomy_fn ID_TO_TAXONOMY_FN
-
-t ID_TO_TAXONOMY_FP, --id_to_taxonomy_fp ID_TO_TAXONOMY_FP
-
-t INPUT_TREE, --input_tree INPUT_TREE
-
-t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP
-
-t TITLE, --title TITLE
-
-t WALLTIME, --walltime WALLTIME
-
-t, --test
-
-u UNIQUE_OTUS_FN, --unique_otus_fn UNIQUE_OTUS_FN
-
-v, --verbose
- command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15]
-
-w STATS_OUT_FNH, --stats_out_fnh STATS_OUT_FNH
|