[med-svn] r19842 - trunk/packages/sortmerna/trunk/debian/man

Wed Aug 5 12:54:26 UTC 2015

Author: tille
Date: 2015-08-05 12:54:25 +0000 (Wed, 05 Aug 2015)
New Revision: 19842

Modified:
   trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1
   trunk/packages/sortmerna/trunk/debian/man/sortmerna.1
Log:
Enhance manpages


Modified: trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1
===================================================================

--- trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1	2015-08-05 12:00:07 UTC (rev 19841)
+++ trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1	2015-08-05 12:54:25 UTC (rev 19842)
@@ -25,17 +25,16 @@
 .TP
 \fB\-\-ref\fR \fISTRING,STRING\fR
 FASTA reference file, index file
-.TP
+.br
 Example:
-.IP
+.br
 \fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1\fP
-.TP
+.br
 If passing multiple reference sequence files, separate them by ':'
-.TP
+.br
 Example:
-.IP
-\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1:/path/to/file2.fasta,path/to/index2\fP
-.IP
+.br
+\fB\-\-ref\fR \fI/path/f1.fasta,/path/index1:/path/f2.fasta,path/index2\fP
 .SS OPTIONAL OPTIONS
 .TP
 \fB\-\-fast\fR \fIBOOL\fR

Modified: trunk/packages/sortmerna/trunk/debian/man/sortmerna.1
===================================================================
--- trunk/packages/sortmerna/trunk/debian/man/sortmerna.1	2015-08-05 12:00:07 UTC (rev 19841)
+++ trunk/packages/sortmerna/trunk/debian/man/sortmerna.1	2015-08-05 12:54:25 UTC (rev 19842)
@@ -25,41 +25,41 @@
 .TP
 \fB\-\-ref\fR \fISTRING,STRING\fR
 FASTA reference file, index file
-.TP
+.br
 Example:
-.IP
+.br
 \fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1\fP
-.TP
+.br
 If passing multiple reference sequence files, separate them by ':'
-.TP
+.br
 Example:
-.IP
-\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1:/path/to/file2.fasta,path/to/index2\fP
+.br
+\fB\-\-ref\fR \fI/path/f1.fasta,/path/index1:/path/f2.fasta,path/index2\fP
 .TP
-\fB\-\-reads\fR \fBSTRING\fR
+\fB\-\-reads\fR \fISTRING\fR
 FASTA/FASTQ reads file
 .TP
-\fB\-\-aligned\fR \fBSTRING\fR
+\fB\-\-aligned\fR \fISTRING\fR
 aligned reads filepath + base file name
 (appropriate extension will be added)
 .SS COMMON OPTIONS
 .TP
-\fB\-\-other\fR \fBSTRING\fR
+\fB\-\-other\fR \fISTRING\fR
 rejected reads filepath + base file name
 (appropriate extension will be added)
 .TP
-\fB\-\-fastx\fR \fBBOOL\fR
+\fB\-\-fastx\fR \fIBOOL\fR
 output FASTA/FASTQ fil (default: off,
 for aligned and/or rejected reads)
 .TP
-\fB\-\-sam\fR \fBBOOL\fR
+\fB\-\-sam\fR \fIBOOL\fR
 output SAM alignmen (default: off,
 for aligned reads only)
 .TP
-\fB\-\-SQ\fR \fBBOOL\fR
+\fB\-\-SQ\fR \fIBOOL\fR
 add SQ tags to the SAM fil (default: off)
 .TP
-\fB\-\-blast\fR \fBINT\fR
+\fB\-\-blast\fR \fIINT\fR
 output alignments in various Blast\-like formats
 .br
 0 \- pairwise
@@ -70,21 +70,21 @@
 .br
 3 \- tabular + columns for CIGAR and query coverage
 .TP
-\fB\-\-log\fR \fBBOOL\fR
+\fB\-\-log\fR \fIBOOL\fR
 output overall statistic (default: off)
 .TP
-\fB\-\-num_alignments\fR \fBINT\fR
+\fB\-\-num_alignments\fR \fIINT\fR
 report first INT alignments per read reaching E\-value (default: -1,
 \fB\-\-num_alignments\fR 0 signifies all alignments will be output)
 .TP
 \fIor\fR (default)
 .TP
-\fB\-\-best\fR \fBINT\fR
+\fB\-\-best\fR \fIINT\fR
 report INT best alignments per read reaching E\-value (default: 1)
 by searching \fB\-\-min_lis\fR \fIINT\fR candidate alignments
 (\fB\-\-best\fR 0 signifies all candidate alignments will be searched)
 .TP
-\fB\-\-min_lis\fR \fBINT\fR
+\fB\-\-min_lis\fR \fIINT\fR
 search all alignments having the first INT longest LIS (default: 2)
 LIS stands for Longest Increasing Subsequence, it is
 computed using seeds' positions to expand hits into
@@ -94,93 +94,93 @@
 output null alignment strings for non\-aligned reads (default: off)
 to SAM and/or BLAST tabular files
 .TP
-\fB\-\-paired_in\fR \fBBOOL\fR
+\fB\-\-paired_in\fR \fIBOOL\fR
 both paired\-end reads go in \fB\-\-aligned\fR fasta/q file (default: off,
 interleaved reads only, see Section 4.2.4 of User Manual)
 .TP
-\fB\-\-paired_out\fR \fBBOOL\fR
+\fB\-\-paired_out\fR \fIBOOL\fR
 both paired\-end reads go in \fB\-\-other\fR fasta/q file (default: off,
 interleaved reads only, see Section 4.2.4 of User Manual)
 .TP
-\fB\-\-match\fR \fBINT\fR
+\fB\-\-match\fR \fIINT\fR
 SW score (positive integer) for a match (default: 2)
 .TP
-\fB\-\-mismatch\fR \fBINT\fR
+\fB\-\-mismatch\fR \fIINT\fR
 SW penalty (negative integer) for a mismatch (default: -3)
 .TP
-\fB\-\-gap_open\fR \fBINT\fR
+\fB\-\-gap_open\fR \fIINT\fR
 SW penalty (positive integer) for introducing a gap (default: 5)
 .TP
-\fB\-\-gap_ext\fR \fBINT\fR
+\fB\-\-gap_ext\fR \fIINT\fR
 SW penalty (positive integer) for extending a gap (default: 2)
 .TP
-\fB\-N\fR \fBINT\fR
+\fB\-N\fR \fIINT\fR
 SW penalty for ambiguous letters (N's) (default: scored as \fB\-\-mismatch\fR)
 .TP
-\fB\-F\fR \fBBOOL\fR
+\fB\-F\fR \fIBOOL\fR
 search only the forward strand (default: off)
 .TP
-\fB\-R\fR \fBBOOL\fR
+\fB\-R\fR \fIBOOL\fR
 search only the reverse\-complementary strand (default: off)
 .TP
-\fB\-a\fR \fBINT\fR
+\fB\-a\fR \fIINT\fR
 number of threads to use  (default: 1)
 .TP
-\fB\-e\fR \fBDOUBLE\fR
+\fB\-e\fR \fIDOUBLE\fR
 E\-value threshold  (default: 1)
 .TP
-\fB\-m\fR \fBINT\fR
+\fB\-m\fR \fIINT\fR
 INT Mbytes for loading the reads into memory (default: 1024,
 maximum \fB\-m\fR INT is 5872)
 .TP
-\fB\-v\fR \fBBOOL\fR
+\fB\-v\fR \fIBOOL\fR
 verbose  (default: off)
 .SS OTU PICKING OPTIONS
 .TP
-\fB\-\-id\fR \fBDOUBLE\fR
+\fB\-\-id\fR \fIDOUBLE\fR
 %id similarity threshold (the alignment must
 still pass the E\-value threshold, default: 0.97)
 .TP
-\fB\-\-coverage\fR \fBDOUBLE\fR
+\fB\-\-coverage\fR \fIDOUBLE\fR
 %query coverage threshold (the alignment must
 still pass the E\-value threshold, default: 0.97)
 .TP
-\fB\-\-de_novo_otu\fR \fBBOOL\fR
+\fB\-\-de_novo_otu\fR \fIBOOL\fR
 FASTA/FASTQ file for reads matching database < %id
 .br
 (set using \fB\-\-id\fR) and < %cov (set using \fB\-\-coverage\fR)
 .br
 (alignment must still pass the E\-value threshold, default: off)
 .TP
-\fB\-\-otu_map\fR \fBBOOL\fR
+\fB\-\-otu_map\fR \fIBOOL\fR
 output OTU map (input to QIIME's make_otu_table.py, default: off)
 
 .SS ADVANCED OPTIONS
 .P
 see SortMeRNA user manual for more details
 .TP
-\fB\-\-passes\fR \fBINT\fR
+\fB\-\-passes\fR \fIINT\fR
 three intervals at which to place the seed on the read
 (L is the seed length set in indexdb_rna(1), default: L,L/2,3)
 .TP
-\fB\-\-edges\fR \fBINT\fR
+\fB\-\-edges\fR \fIINT\fR
 number (or percent if INT followed by % sign) of
 nucleotides to add to each edge of the read
 prior to SW local alignment (default: 4)
 .TP
-\fB\-\-num_seeds\fR \fBINT\fR
+\fB\-\-num_seeds\fR \fIINT\fR
 number of seeds matched before searching for candidate LIS (default: 2)
 .TP
-\fB\-\-full_search\fR \fBBOOL\fR
+\fB\-\-full_search\fR \fIBOOL\fR
 search for all 0\-error and 1\-error seed matches in the index rather than stopping
 after finding a 0\-error match (<1% gain in
 sensitivity with up four\-fold decrease in speed, default: off)
 .TP
-\fB\-\-pid\fR \fBBOOL\fR
+\fB\-\-pid\fR \fIBOOL\fR
 add pid to output file names (default: off)
 .TP
-\fB\-h\fR \fBBOOL\fR
+\fB\-h\fR \fIBOOL\fR
 help
 .TP
-\fB\-\-version\fR \fBBOOL\fR
+\fB\-\-version\fR \fIBOOL\fR
 SortMeRNA version number


