From 4bc4954b2476397c29b57d20bd3eb47926b30860 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 6 Mar 2014 11:05:09 -0500 Subject: input-filelist --- src/c/multifasta_to_otu.1 | 5 +++++ src/c/multifasta_to_otu.c | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1 index 748e9e9..d047ad1 100644 --- a/src/c/multifasta_to_otu.1 +++ b/src/c/multifasta_to_otu.1 @@ -5,6 +5,8 @@ multifasta_to_otu \- create a QIIME OTU table based on Quikr results. .B multifasta_to_otu .RB [ \-i .IR input-directory ] +.RB [ \-f +.IR input-filelist ] .RB [ \-s .IR sensing-matrix] .RB [ \-k @@ -29,6 +31,9 @@ number of times a specimen was seen in all of the samples. .B \-i, --input-directory the directory containing the samples' fasta files of reads (note each fasta file should correspond to a separate sample) .TP +.B \-f, --input-filelist +a file containing list of fasta files to process seperated by newline (same rules apply as input-directory) +.TP .B \-s, --sensing-matrix location of the sensing matrix. .TP diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index b6b0182..32cc3e9 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -20,7 +20,7 @@ #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-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.\n\n-V, --version\n\tprint version." +#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, --input-filelist\n\ta file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\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.\n\n-V, --version\n\tprint version." static int cmp (const void * a, const void * b) { return ( *(double*)a - *(double*)b ); -- cgit v1.2.3