update documention to include current arguments

1 files changed, 24 insertions, 16 deletions

diff --git a/doc/cli.markdown b/doc/cli.markdown
index 587d014..ac5a231 100644
--- a/doc/cli.markdown
+++ b/doc/cli.markdown
@@ -4,6 +4,9 @@ module and the matlab implementation. The advantage of this is ease of scripting
 and job management, as well as faster processing and lower memory usage. These 
 utilities are written in C and utilize OpenMP for multithreading.
 
+For more in-depth information about these tools please refer to their
+respective manual pages.
+
 ## Quikr\_train ##
 The quikr\_train is a tool to train a database for use with the quikr tool.
 Before running the quikr utility, you need to generate the sensing matrix.
@@ -17,6 +20,7 @@ function.
       -o, --output, the sensing matrix (text file)
       -k, --kmer, specifiy wha size of kmer to use. (default value is 6)
       -v, --verbose, verbose mode.
+      -V, --version, print version.
 
 ### Example ###
 Here is an example on how to train a database. This uses the -z flag to compress
@@ -35,12 +39,15 @@ input FASTA file. You need to train a matrix or download a new matrix
 quikr returns the solution vector as a csv file.
 
     quikr's arguments:
-      -f, --fasta, the sample's fasta file of NGS READS
-      -o, --output OTU\_FRACTION\_PRESENT, a vector representing the percentage of
-          database sequence's presence in sample (csv output)
-      -s, --sensing-matrix the sensing matrix. (generated by quikr\_train)
-      -l, --lambda, the lambda size. (the default lambda value is 10,000)
-      -k, --kmer, this specifies the size of the kmer to use (default is 6)
+    -i, --input the sample's fasta file of NGS READS (fasta format)
+    -f, --sensing-fasta location of the fasta file database used to create the sensing matrix (fasta format)
+    -s, --sensing-matrix location of the sensing matrix. (trained from quikr_train)
+    -k, --kmer specify what size of kmer to use. (default value is 6)
+    -l, --lambda lambda value to use. (default value is 10000)
+    -o, --output OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)
+    -v, --verbose verbose mode.
+    -V, --version print version.
+    -d, --debug debug mode, read manpage for more details
 
 ## Multifasta\_to\_otu ##
 The Multifasta\_to\_otu tool is a handy wrapper for quikr which lets the user
@@ -63,16 +70,17 @@ with aspecified number of jobs. Otherwise python with run one job per cpu core.
 ### Usage ###
 
     multifasta\_to\_otu's arguments:
-      -i, --input, the directory containing the samples' fasta files of
-      reads (note each fasta file should correspond to a separate sample)
-      -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)
-      -s, --sensing-matrix, the sensing matrix
-      -f, --sensing-fasta, the fasta file database of sequences
-      -l, --lambda, specify what size of lambda to use (the default value is 10,000)
-      -k, --kmer, specify what size of kmer to use, (default value is 6)
-      -j, --jobs, specifies how many jobs to run at once, (default=number of CPUs)
+    -i, --input-directory the directory containing the samples' fasta files of 
+    reads (note each file should correspond to a separate sample)
+    -f, --sensing-fasta location of the fasta file database used to create the sensing matrix (fasta format)
+    -s, --sensing-matrix location of the sensing matrix. (sensing from quikr_train)
+    -k, --kmer specify what size of kmer to use. (default value is 6)
+    -l, --lambda lambda value to use. (default value is 10000)
+    -j, --jobs specifies how many jobs to run at once. (default value is the number of CPUs)
+    -o, --output the 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)
+    -v, --verbose verbose mode.
+    -V, --version  print version.
 
 ### Post-processing of Multifasta\_to\_otu  ###