runMannWhitneyCommandLine.txt

# first line is the description of what the program does.
# subsequent lines list positional arguments (PA), then key-value (KV)arguments (KVA).
# Positional line:
# PA_name|PA_Description|Is_out_dir|Is_Dir|Check_Directory|Is_file|Check_File|||
# Key/Value Line:
# KVA_name|KVA_Description|Is_out_dir|Is_Dir|Check_Directory|Is_file|Check_File|alternate_KVA_name|default value|type
# in_targets_with_hits| input file of targets that have at least one hit_in_db|0|0|0|1|1|||
# Example below
Read in file of gene expression or GSVA scores(genes in rows, samples in columns with headers) and perform mann-whitney test on specified samples
out_dir|Top level directory that holds all the results|1|1|1|0|0|||
in_file|input file of gene expression or GSVA scores|0|0|0|1|1|||
cond1_names|header names of condition 1 samples (comma-separated)|0|0|0|0|0|||
cond2_names|header names of condition 1 samples (comma-separated)|0|0|0|0|0|||
-paired|paired data|0|0|0|0|0|--paired_data|BOOLEANFALSE|
-show_w|show wilks p-value|0|0|0|0|0|--show_wilks|BOOLEANFALSE|
-MW|Run Mann-Whitney test (default is t-test)|0|0|0|0|0|--mann_whitney|BOOLEANFALSE|
-use_pval|Permute using the p-value (default is to permute using the statistic)|0|0|0|0|0|--use_pval_for_perm|BOOLEANFALSE|
-perm|Permute (default is to NOT permute)|0|0|0|0|0|--permute|BOOLEANFALSE|
-shuf_labels|NOT CURRENTLY WORKING  Permute based on shuffling labels (default is to NOT permute based on shuffling labels)|0|0|0|0|0|--shuffle_labels|BOOLEANFALSE|
-dbg|debug|0|0|0|0|0|--debug|BOOLEANFALSE|
-wel_t|Do Welch t test|0|0|0|0|0|--welch_t|BOOLEANFALSE|
-alt|alternative for test. Must be: two-sided, less, or greater|0|0|0|0|0|--alternative|two-sided|