-
--dpi DPI
- command line option, [1]
-
--output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN
- command line option
-
--p1 P1
- command line option
-
--p2 P2
- command line option
-
--pc_order PC_ORDER
- command line option
-
--plot_title PLOT_TITLE
- command line option
-
--save_lda_input SAVE_LDA_INPUT
- command line option
-
--scaling_factor SCALING_FACTOR
- command line option
-
--stabilize_variance
- command line option, [1]
-
--x_limits X_LIMITS X_LIMITS
- command line option
-
--y_limits Y_LIMITS Y_LIMITS
- command line option
-
--z_limits Z_LIMITS Z_LIMITS
- command line option
-
-a {MRA,NMRA,raw}, --analysis_metric {MRA,NMRA,raw}
- command line option
-
-b COLORBY, --colorby COLORBY
- command line option
-
-c COLOR_BY, --color_by COLOR_BY
- command line option
-
-c COLORS, --colors COLORS
- command line option
-
-c MAP_CATEGORIES, --map_categories MAP_CATEGORIES
- command line option
-
-c MAP_CATEGORY, --map_category MAP_CATEGORY
- command line option, [1]
-
-c {shannon,chao1,jaccard} [{shannon,chao1,jaccard} ...]
- command line option
-
-d NAMES_COLORS_IDS_FN, --names_colors_ids_fn NAMES_COLORS_IDS_FN
- command line option
-
-d {2,3}, --dimensions {2,3}
- command line option
-
-e OUTPUT_TRE, --output_tre OUTPUT_TRE
- command line option
-
-g GROUP_BY [GROUP_BY ...], --group_by GROUP_BY [GROUP_BY ...]
- command line option
-
-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]
-
-i ASSIGNED_TAXONOMY_FN, --assigned_taxonomy_fn ASSIGNED_TAXONOMY_FN
- command line option
-
-i BIOM_TSV, --biom_tsv BIOM_TSV
- command line option
-
-i COORD_FP, --coord_fp COORD_FP
- command line option
-
-i INPUT_ASSIGNED_TAXONOMY, --input_assigned_taxonomy INPUT_ASSIGNED_TAXONOMY
- command line option
-
-i INPUT_BIOM_FP, --input_biom_fp INPUT_BIOM_FP
- command line option, [1]
-
-i INPUT_FASTA_FN, --input_fasta_fn INPUT_FASTA_FN
- command line option, [1]
-
-i INPUT_FNA [INPUT_FNA ...], --input_fna INPUT_FNA [INPUT_FNA ...]
- command line option
-
-i OTU_ID_FP, --otu_id_fp OTU_ID_FP
- command line option
-
-i OTU_MAP, --otu_map OTU_MAP
- command line option
-
-i OTU_TABLE, --otu_table OTU_TABLE
- command line option, [1]
-
-i REP_SET_FP, --rep_set_fp REP_SET_FP
- command line option
-
-i SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN
- command line option
-
-k SAMPLES_TO_KEEP_FP, --samples_to_keep_fp SAMPLES_TO_KEEP_FP
- command line option
-
-L {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}
- command line option
-
-l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}
- command line option, [1]
|
-
-m MAP_FP, --map_fp MAP_FP
- command line option, [1]
-
-m MAPPING, --mapping MAPPING
- command line option, [1], [2]
-
-m MAPPING_FN, --mapping_fn MAPPING_FN
- command line option
-
-n JOB_NAME, --job_name JOB_NAME
- command line option
-
-n NON_UNIQUE_OTU_MATRIX, --non_unique_otu_matrix NON_UNIQUE_OTU_MATRIX
- command line option
-
-n NON_UNIQUE_OUTPUT_FILE, --non_unique_output_file NON_UNIQUE_OUTPUT_FILE
- command line option
-
-n NUM_OUTPUT_FILES, --num_output_files NUM_OUTPUT_FILES
- command line option
-
-o ASSIGNED_TAXONOMY_FP, --assigned_taxonomy_fp ASSIGNED_TAXONOMY_FP
- command line option
-
-o CONDENSED_SEQS_OTUS_FILE, --condensed_seqs_otus_file CONDENSED_SEQS_OTUS_FILE
- command line option
-
-o OUT_FP, --out_fp OUT_FP
- command line option, [1]
-
-o OUTPUT_BIOM_FP, --output_biom_fp OUTPUT_BIOM_FP
- command line option
-
-o OUTPUT_CSV_FP, --output_csv_fp OUTPUT_CSV_FP
- command line option
-
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
- command line option, [1]
-
-o OUTPUT_FILTERED_REP_SET_FN, --output_filtered_rep_set_fn OUTPUT_FILTERED_REP_SET_FN
- command line option
-
-o OUTPUT_FN, --output_fn OUTPUT_FN
- command line option
-
-o OUTPUT_FP, --output_fp OUTPUT_FP
- command line option, [1]
-
-o OUTPUT_ITOL_TABLE, --output_itol_table OUTPUT_ITOL_TABLE
- command line option
-
-o OUTPUT_OTU_MAP_FP, --output_otu_map_fp OUTPUT_OTU_MAP_FP
- command line option
-
-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
- command line option
-
-o OUTPUT_PRUNED_OTUS_FN, --output_pruned_otus_fn OUTPUT_PRUNED_OTUS_FN
- command line option
-
-p IMAGE_TYPE, --image_type IMAGE_TYPE
- command line option
-
-p PERCENT_OF_SAMPLES, --percent_of_samples PERCENT_OF_SAMPLES
- command line option
-
-p PRUNED_OUTPUT_FILE, --pruned_output_file PRUNED_OUTPUT_FILE
- command line option
-
-q QUALITY_FN, --quality_fn QUALITY_FN
- command line option
-
-r REP_SET_FN, --rep_set_fn REP_SET_FN
- command line option, [1]
-
-s PERCENT_OF_SEQUENCES, --percent_of_sequences PERCENT_OF_SEQUENCES
- command line option
-
-s POINT_SIZE, --point_size POINT_SIZE
- command line option
-
-s SEQS_OTUS, --seqs_otus SEQS_OTUS
- command line option
-
-s SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN
- command line option
-
-t ID_TO_TAXONOMY_FN, --id_to_taxonomy_fn ID_TO_TAXONOMY_FN
- command line option
-
-t ID_TO_TAXONOMY_FP, --id_to_taxonomy_fp ID_TO_TAXONOMY_FP
- command line option
-
-t INPUT_TREE, --input_tree INPUT_TREE
- command line option
-
-t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP
- command line option
-
-t TITLE, --title TITLE
- command line option
-
-t WALLTIME, --walltime WALLTIME
- command line option
-
-t, --test
- command line option
-
-u UNIFRAC, --unifrac UNIFRAC
- command line option
-
-u UNIQUE_OTUS_FN, --unique_otus_fn UNIQUE_OTUS_FN
- command line option
-
-v, --verbose
- command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]
|