[med-svn] [sortmerna] 07/14: Enhance manpages
Andreas Tille
tille at debian.org
Mon Sep 25 11:21:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sortmerna.
commit f751e8fb05c3526a062c31f14ed8b7c22bc8ae6a
Author: Andreas Tille <tille at debian.org>
Date: Wed Aug 5 12:54:25 2015 +0000
Enhance manpages
---
debian/man/indexdb_rna.1 | 13 ++++----
debian/man/sortmerna.1 | 82 ++++++++++++++++++++++++------------------------
2 files changed, 47 insertions(+), 48 deletions(-)
diff --git a/debian/man/indexdb_rna.1 b/debian/man/indexdb_rna.1
index c4a818f..4ed6a95 100644
--- a/debian/man/indexdb_rna.1
+++ b/debian/man/indexdb_rna.1
@@ -25,17 +25,16 @@ BLAST-like alignments.
.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
diff --git a/debian/man/sortmerna.1 b/debian/man/sortmerna.1
index babb438..f0e8786 100644
--- a/debian/man/sortmerna.1
+++ b/debian/man/sortmerna.1
@@ -25,41 +25,41 @@ BLAST-like alignments.
.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 @@ output alignments in various Blast\-like formats
.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 @@ longer matches prior to Smith\-Waterman alignment.
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
--
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