diff options
Diffstat (limited to 'src/c')
| -rw-r--r-- | src/c/multifasta_to_otu.1 | 2 | ||||
| -rw-r--r-- | src/c/multifasta_to_otu.c | 2 | ||||
| -rw-r--r-- | src/c/quikr.c | 2 |
3 files changed, 3 insertions, 3 deletions
diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1 index 7878ef0..29fe5d7 100644 --- a/src/c/multifasta_to_otu.1 +++ b/src/c/multifasta_to_otu.1 @@ -47,7 +47,7 @@ lambda value to use. (default value is 10000) specifies how many jobs to run at once. (default value is the number of CPUs) .TP .B \-o, --otu-table -the OTU table, with OTU_FRACTION_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or sequence table if not OTU's) +the OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or sequence table if not OTU's) .TP .B \-v, --verbose verbose mode. diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 0d81e13..2f4bf87 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -13,7 +13,7 @@ #define sensing_matrix(i,j) (sensing_matrix[width*i + j]) #define solutions(i,j) (solutions[sequences*i+ j]) -#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with OTU_FRACTION_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode." +#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode." int main(int argc, char **argv) { diff --git a/src/c/quikr.c b/src/c/quikr.c index 123756c..17d6480 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -12,7 +12,7 @@ #include "quikr_functions.h" #define sensing_matrix(i,j) (sensing_matrix[width*i + j]) -#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tthe sensing matrix. (a gzip'd text file)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, read manpage for more details" +#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, read manpage for more details" int main(int argc, char **argv) { |