[med-svn] r19841 - in trunk/packages/sortmerna/trunk/debian: . man

Andreas Tille tille at moszumanska.debian.org
Wed Aug 5 12:00:08 UTC 2015 

Author: tille
Date: 2015-08-05 12:00:07 +0000 (Wed, 05 Aug 2015)
New Revision: 19841

Added:
   trunk/packages/sortmerna/trunk/debian/man/
   trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1
   trunk/packages/sortmerna/trunk/debian/man/sortmerna.1
   trunk/packages/sortmerna/trunk/debian/manpages
Log:
Add manpages


Added: trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1
===================================================================
--- trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1	                        (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/man/indexdb_rna.1	2015-08-05 12:00:07 UTC (rev 19841)
@@ -0,0 +1,64 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
+.TH INDEXDB_RNA "1" "August 2015" "indexdb_rna 2.0" "User Commands"
+.SH NAME
+indexdb_rna \- tool for filtering, mapping and OTU-picking NGS reads (indexdb)
+.SH SYNOPSIS
+.B indexdb_rna
+\fB\-\-ref\fR db.fasta,db.idx [OPTIONS]
+.SH DESCRIPTION
+.P
+SortMeRNA is a biological sequence analysis tool for filtering, mapping and
+OTU-picking NGS reads. The core algorithm is based on approximate seeds and
+allows for fast and sensitive analyses of nucleotide sequences. The main
+application of SortMeRNA is filtering rRNA from metatranscriptomic data.
+Additional applications include OTU-picking and taxonomy assignation available
+through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
+.P
+SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
+multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
+two files specified by the user. Optionally, it can provide high quality local
+alignments of rRNA reads against the rRNA database. SortMeRNA works with
+Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
+BLAST-like alignments.
+.SH OPTIONS
+.SS MANDATORY OPTIONS
+.TP
+\fB\-\-ref\fR \fISTRING,STRING\fR
+FASTA reference file, index file
+.TP
+Example:
+.IP
+\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1\fP
+.TP
+If passing multiple reference sequence files, separate them by ':'
+.TP
+Example:
+.IP
+\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1:/path/to/file2.fasta,path/to/index2\fP
+.IP
+.SS OPTIONAL OPTIONS
+.TP
+\fB\-\-fast\fR \fIBOOL\fR
+suggested option for aligning ~99% related species (default: off)
+.TP
+\fB\-\-sensitive\fR \fIBOOL\fR
+suggested option for aligning ~75\-98% related species (default: on)
+.TP
+\fB\-\-tmpdir\fR \fISTRING\fR
+directory where to write temporary files
+.TP
+\fB\-m\fR \fIINT\fR
+the amount of memory (in Mbytes) for building the index (default: 3072)
+.TP
+\fB\-L\fR \fIINT\fR
+seed length (default: 18)
+.TP
+\fB\-\-max_pos\fR \fIINT\fR
+maximum number of positions to store for each unique L\-mer (default: 10000,
+setting \fB\-\-max_pos\fR 0 will store all positions)
+.TP
+\fB\-v\fR \fIBOOL\fR
+verbose
+.TP
+\fB\-h\fR \fIBOOL\fR
+help       

Added: trunk/packages/sortmerna/trunk/debian/man/sortmerna.1
===================================================================
--- trunk/packages/sortmerna/trunk/debian/man/sortmerna.1	                        (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/man/sortmerna.1	2015-08-05 12:00:07 UTC (rev 19841)
@@ -0,0 +1,186 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH SORTMERNA "1" "August 2015" "sortmerna 2.0" "User Commands"
+.SH NAME
+sortmerna \- tool for filtering, mapping and OTU-picking NGS reads
+.SH SYNOPSIS
+.B sortmerna
+\fB\-\-ref\fR db.fasta,db.idx \fB\-\-reads\fR file.fa \fB\-\-aligned\fR base_name_output [OPTIONS]
+.SH DESCRIPTION
+.P
+SortMeRNA is a biological sequence analysis tool for filtering, mapping and
+OTU-picking NGS reads. The core algorithm is based on approximate seeds and
+allows for fast and sensitive analyses of nucleotide sequences. The main
+application of SortMeRNA is filtering rRNA from metatranscriptomic data.
+Additional applications include OTU-picking and taxonomy assignation available
+through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
+.P
+SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
+multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
+two files specified by the user. Optionally, it can provide high quality local
+alignments of rRNA reads against the rRNA database. SortMeRNA works with
+Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
+BLAST-like alignments.
+.SH OPTIONS
+.SS MANDATORY OPTIONS
+.TP
+\fB\-\-ref\fR \fISTRING,STRING\fR
+FASTA reference file, index file
+.TP
+Example:
+.IP
+\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1\fP
+.TP
+If passing multiple reference sequence files, separate them by ':'
+.TP
+Example:
+.IP
+\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1:/path/to/file2.fasta,path/to/index2\fP
+.TP
+\fB\-\-reads\fR \fBSTRING\fR
+FASTA/FASTQ reads file
+.TP
+\fB\-\-aligned\fR \fBSTRING\fR
+aligned reads filepath + base file name
+(appropriate extension will be added)
+.SS COMMON OPTIONS
+.TP
+\fB\-\-other\fR \fBSTRING\fR
+rejected reads filepath + base file name
+(appropriate extension will be added)
+.TP
+\fB\-\-fastx\fR \fBBOOL\fR
+output FASTA/FASTQ fil (default: off,
+for aligned and/or rejected reads)
+.TP
+\fB\-\-sam\fR \fBBOOL\fR
+output SAM alignmen (default: off,
+for aligned reads only)
+.TP
+\fB\-\-SQ\fR \fBBOOL\fR
+add SQ tags to the SAM fil (default: off)
+.TP
+\fB\-\-blast\fR \fBINT\fR
+output alignments in various Blast\-like formats
+.br
+0 \- pairwise
+.br
+1 \- tabular (Blast \fB\-m\fR 8 format)
+.br
+2 \- tabular + column for CIGAR
+.br
+3 \- tabular + columns for CIGAR and query coverage
+.TP
+\fB\-\-log\fR \fBBOOL\fR
+output overall statistic (default: off)
+.TP
+\fB\-\-num_alignments\fR \fBINT\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
+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
+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
+longer matches prior to Smith\-Waterman alignment.
+.TP
+\fB\-\-print_all_reads\fR
+output null alignment strings for non\-aligned reads (default: off)
+to SAM and/or BLAST tabular files
+.TP
+\fB\-\-paired_in\fR \fBBOOL\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
+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
+SW score (positive integer) for a match (default: 2)
+.TP
+\fB\-\-mismatch\fR \fBINT\fR
+SW penalty (negative integer) for a mismatch (default: -3)
+.TP
+\fB\-\-gap_open\fR \fBINT\fR
+SW penalty (positive integer) for introducing a gap (default: 5)
+.TP
+\fB\-\-gap_ext\fR \fBINT\fR
+SW penalty (positive integer) for extending a gap (default: 2)
+.TP
+\fB\-N\fR \fBINT\fR
+SW penalty for ambiguous letters (N's) (default: scored as \fB\-\-mismatch\fR)
+.TP
+\fB\-F\fR \fBBOOL\fR
+search only the forward strand (default: off)
+.TP
+\fB\-R\fR \fBBOOL\fR
+search only the reverse\-complementary strand (default: off)
+.TP
+\fB\-a\fR \fBINT\fR
+number of threads to use  (default: 1)
+.TP
+\fB\-e\fR \fBDOUBLE\fR
+E\-value threshold  (default: 1)
+.TP
+\fB\-m\fR \fBINT\fR
+INT Mbytes for loading the reads into memory (default: 1024,
+maximum \fB\-m\fR INT is 5872)
+.TP
+\fB\-v\fR \fBBOOL\fR
+verbose  (default: off)
+.SS OTU PICKING OPTIONS
+.TP
+\fB\-\-id\fR \fBDOUBLE\fR
+%id similarity threshold (the alignment must
+still pass the E\-value threshold, default: 0.97)
+.TP
+\fB\-\-coverage\fR \fBDOUBLE\fR
+%query coverage threshold (the alignment must
+still pass the E\-value threshold, default: 0.97)
+.TP
+\fB\-\-de_novo_otu\fR \fBBOOL\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
+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
+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
+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
+number of seeds matched before searching for candidate LIS (default: 2)
+.TP
+\fB\-\-full_search\fR \fBBOOL\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
+add pid to output file names (default: off)
+.TP
+\fB\-h\fR \fBBOOL\fR
+help
+.TP
+\fB\-\-version\fR \fBBOOL\fR
+SortMeRNA version number

Added: trunk/packages/sortmerna/trunk/debian/manpages
===================================================================
--- trunk/packages/sortmerna/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/manpages	2015-08-05 12:00:07 UTC (rev 19841)
@@ -0,0 +1 @@
+debian/man/*.1

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