[med-svn] [Git][med-team/mecat2][master] Write manpages
Shayan Doust
gitlab at salsa.debian.org
Fri Jul 3 18:20:55 BST 2020
Shayan Doust pushed to branch master at Debian Med / mecat2
Commits:
ee5920ba by Shayan Doust at 2020-07-03T18:20:33+01:00
Write manpages
- - - - -
7 changed files:
- + debian/mans/fsa_assemble.1
- + debian/mans/fsa_ctg_bridge.1
- + debian/mans/fsa_ol_filter.1
- + debian/mans/fsa_rd_stat.1
- + debian/mans/mecat.1
- + debian/mans/mecat2pcan.1
- + debian/mecat2.manpages
Changes:
=====================================
debian/mans/fsa_assemble.1
=====================================
@@ -0,0 +1,142 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FSA_ASSEMBLE "1" "July 2020" "Constructs contigs from filtered overlaps and corrected reads." "User Commands"
+.SH NAME
+fsa_assemble \- Constructs contigs from filtered overlaps and corrected reads
+.SH SYNOPSIS
+.B fsa_assemble
+[\fI\,options\/\fR] \fI\,filterd_overlaps\/\fR
+.SH DESCRIPTION
+Constructs contigs from filtered overlaps and corrected reads.
+.SH OPTIONS
+.HP
+\fB\-\-min_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of reads
+default: 0
+.HP
+\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps
+default: 0
+.HP
+\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps
+default: 0
+.HP
+\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of contigs
+default: 500
+.HP
+\fB\-\-read_file\fR=\fI\,STRING\/\fR
+.IP
+read filename
+default: ""
+.HP
+\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
+.IP
+overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
+default: ""
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-select_branch=\fR"no|best"
+.IP
+selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
+default: "no"
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 1
+.HP
+\fB\-\-dump\fR=\fI\,INT\/\fR
+.IP
+for testing, dump intermediate files
+default: 0
+.HP
+\fB\-\-run_mode\fR=\fI\,INT\/\fR
+.IP
+for testing
+default: 4
+.HP
+\fB\-\-lfc\fR
+.IP
+deprecated, for testing
+.HP
+\fB\-\-remove_chimer\fR
+.IP
+deprecated, remove chimer node
+.PP
+Usage: fsa_assemble [options] filterd_overlaps
+.IP
+filterd_overlaps
+.IP
+input filename
+.HP
+\fB\-\-min_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of reads
+default: 0
+.HP
+\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps
+default: 0
+.HP
+\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps
+default: 0
+.HP
+\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of contigs
+default: 500
+.HP
+\fB\-\-read_file\fR=\fI\,STRING\/\fR
+.IP
+read filename
+default: ""
+.HP
+\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
+.IP
+overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
+default: ""
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-select_branch=\fR"no|best"
+.IP
+selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
+default: "no"
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 1
+.HP
+\fB\-\-dump\fR=\fI\,INT\/\fR
+.IP
+for testing, dump intermediate files
+default: 0
+.HP
+\fB\-\-run_mode\fR=\fI\,INT\/\fR
+.IP
+for testing
+default: 4
+.HP
+\fB\-\-lfc\fR
+.IP
+deprecated, for testing
+.HP
+\fB\-\-remove_chimer\fR
+.IP
+deprecated, remove chimer node
=====================================
debian/mans/fsa_ctg_bridge.1
=====================================
@@ -0,0 +1,196 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FSA_CTG_BRIDGE "1" "July 2020" "Bridge contigs" "User Commands"
+.SH NAME
+fsa_ctg_bridge \- Bridge contigs
+.SH SYNOPSIS
+.B fsa_ctg_bridge
+[\fI\,options\/\fR] \fI\,rawreads contigs read2ctg bridged_contigs\/\fR
+.SH DESCRIPTION
+Command line tool to bridge contigs.
+
+
+It takes the following parameters:
+
+.IP
+rawreads
+.IP
+ rawread file
+.IP
+contigs
+.IP
+ The contig file
+.IP
+read2ctg
+.IP
+ The file containing overlaps between rawread and contigs
+.IP
+bridged_contigs
+.IP
+ The output file
+.SH OPTIONS
+.HP
+\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR
+.IP
+filename containing overlaps between contigs
+default: ""
+.HP
+\fB\-\-read_min_length\fR=\fI\,INT\/\fR
+.IP
+minimum rawread length
+default: 10000
+.HP
+\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR
+.IP
+minimum contig length
+default: 500
+.HP
+\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps between rawreads and contigs
+default: 80
+.HP
+\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps between contigs
+default: 95
+.HP
+\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps between rawreads and contigs
+default: 500
+.HP
+\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps between contigs
+default: 100
+.HP
+\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps between rawreads and contigs
+default: 5000
+.HP
+\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps between contigs
+default: 2000
+.HP
+\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR
+.IP
+minimum coverage of links between rawreads and contigs
+default: 4
+.HP
+\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of bridged contig
+default: 500
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-select_branch=\fR"no|best"
+.IP
+selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
+default: "no"
+.HP
+\fB\-\-dump\fR
+.IP
+for testing, dump intermediate files
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 4
+.PP
+Usage: fsa_ctg_bridge [options] rawreads contigs read2ctg bridged_contigs
+.IP
+rawreads
+.IP
+rawread file
+.IP
+contigs
+.IP
+contig file
+.IP
+read2ctg
+.IP
+file containing overlaps between rawread and contigs
+.IP
+bridged_contigs
+.IP
+output file
+.HP
+\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR
+.IP
+filename containing overlaps between contigs
+default: ""
+.HP
+\fB\-\-read_min_length\fR=\fI\,INT\/\fR
+.IP
+minimum rawread length
+default: 10000
+.HP
+\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR
+.IP
+minimum contig length
+default: 500
+.HP
+\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps between rawreads and contigs
+default: 80
+.HP
+\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps between contigs
+default: 95
+.HP
+\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps between rawreads and contigs
+default: 500
+.HP
+\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps between contigs
+default: 100
+.HP
+\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps between rawreads and contigs
+default: 5000
+.HP
+\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps between contigs
+default: 2000
+.HP
+\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR
+.IP
+minimum coverage of links between rawreads and contigs
+default: 4
+.HP
+\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of bridged contig
+default: 500
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-select_branch=\fR"no|best"
+.IP
+selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
+default: "no"
+.HP
+\fB\-\-dump\fR
+.IP
+for testing, dump intermediate files
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 4
=====================================
debian/mans/fsa_ol_filter.1
=====================================
@@ -0,0 +1,189 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FILTERS "1" "July 2020" "Filters out low-quality overlaps for assembling" "User Commands"
+.SH NAME
+Filters \- Low quality overlap filtering
+.SH SYNOPSIS
+.B fsa_ol_filter
+[\fI\,options\/\fR] \fI\,overlaps filtered_overlaps\/\fR
+.SH DESCRIPTION
+Command line tool to filters out low\-quality overlaps prior to assembling.
+
+This takes the following parameters:
+
+.IP
+overlaps
+.IP
+ The input filename
+.IP
+filtered_overlaps
+.IP
+ The resulting ouput filename
+.SH OPTIONS
+.HP
+\fB\-\-min_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of reads
+.IP
+default: 2500
+.HP
+\fB\-\-max_length\fR=\fI\,INT\/\fR
+.IP
+maximum length of reads
+default: 2147483647
+.HP
+\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps
+.IP
+default: 90
+.HP
+\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps
+default: 2500
+.HP
+\fB\-\-max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps, negative number = determined by the program.
+.IP
+default: 10
+.HP
+\fB\-\-min_coverage\fR=\fI\,INT\/\fR
+.IP
+minimum base coverage, negative number = determined by the program.
+default: \fB\-1\fR
+.HP
+\fB\-\-max_coverage\fR=\fI\,INT\/\fR
+.IP
+maximum base coverage, negative number = determined by the program
+default: \fB\-1\fR
+.HP
+\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR
+.IP
+maximum difference of base coverage, negative number = determined by the program
+default: \fB\-1\fR
+.HP
+\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR
+.IP
+discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100\-coverage_discard)th percentile.
+default: 0.01
+.HP
+\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
+.IP
+overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
+default: ""
+.HP
+\fB\-\-bestn\fR=\fI\,INT\/\fR
+.IP
+output best n overlaps on 5' or 3' end for each read
+.IP
+default: 10
+.HP
+\fB\-\-genome_size\fR=\fI\,INT\/\fR
+.IP
+genome size. It determines the maximum length of reads with coverage together
+default: 0
+.HP
+\fB\-\-coverage\fR=\fI\,INT\/\fR
+.IP
+coverage. It determines the maximum length of reads with genome_size together
+default: 0
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 4
+.PP
+Usage: fsa_ol_filter [options] overlaps filtered_overlaps
+.IP
+overlaps
+.IP
+input filename
+.IP
+filtered_overlaps
+.IP
+ouput filename
+.HP
+\fB\-\-min_length\fR=\fI\,INT\/\fR
+.IP
+minimum length of reads
+.IP
+default: 2500
+.HP
+\fB\-\-max_length\fR=\fI\,INT\/\fR
+.IP
+maximum length of reads
+default: 2147483647
+.HP
+\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
+.IP
+minimum identity of overlaps
+.IP
+default: 90
+.HP
+\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
+.IP
+minimum aligned length of overlaps
+default: 2500
+.HP
+\fB\-\-max_overhang\fR=\fI\,INT\/\fR
+.IP
+maximum overhang of overlaps, negative number = determined by the program.
+.IP
+default: 10
+.HP
+\fB\-\-min_coverage\fR=\fI\,INT\/\fR
+.IP
+minimum base coverage, negative number = determined by the program.
+default: \fB\-1\fR
+.HP
+\fB\-\-max_coverage\fR=\fI\,INT\/\fR
+.IP
+maximum base coverage, negative number = determined by the program
+default: \fB\-1\fR
+.HP
+\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR
+.IP
+maximum difference of base coverage, negative number = determined by the program
+default: \fB\-1\fR
+.HP
+\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR
+.IP
+discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100\-coverage_discard)th percentile.
+default: 0.01
+.HP
+\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
+.IP
+overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
+default: ""
+.HP
+\fB\-\-bestn\fR=\fI\,INT\/\fR
+.IP
+output best n overlaps on 5' or 3' end for each read
+.IP
+default: 10
+.HP
+\fB\-\-genome_size\fR=\fI\,INT\/\fR
+.IP
+genome size. It determines the maximum length of reads with coverage together
+default: 0
+.HP
+\fB\-\-coverage\fR=\fI\,INT\/\fR
+.IP
+coverage. It determines the maximum length of reads with genome_size together
+default: 0
+.HP
+\fB\-\-output_directory\fR=\fI\,STRING\/\fR
+.IP
+directory for output files
+default: "."
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+number of threads
+default: 4
=====================================
debian/mans/fsa_rd_stat.1
=====================================
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FSA_RD_STAT "1" "July 2020" "fsa_rd_stat " "User Commands"
+.SH NAME
+fsa_rd_stat \- Reads and outputs the filename of the dataset
+.SH SYNOPSIS
+fsa_rd_stat
+.B [options]
+\fI\,ifname\/\fR
+.SH DESCRIPTION
+.IP
+ifname
+.IP
+read file name
+.SH OPTIONS
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+Number of threads
+default: 4
+.PP
+Usage: [options] ifname
+.IP
+ifname
+.IP
+read file name
+.HP
+\fB\-\-thread_size\fR=\fI\,INT\/\fR
+.IP
+Number of threads
+default: 4
=====================================
debian/mans/mecat.1
=====================================
@@ -0,0 +1,25 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH MECAT "1" "July 2020" "mecat" "User Commands"
+.SH NAME
+mecat \- Generate config file or assemble, trim or correct SMRT data
+.SH SYNOPSIS
+.B mecat
+\fI\,correct|assemble|config cfg_fname\/\fR
+.SH DESCRIPTION
+MECAT (v2) is an ultra-fast and accurate mapping, error correcting and de novo assembly tools for single molecula sequencing (SMRT) reads.
+
+The parameters are defined as below:
+.TP
+correct:
+ Correct rawreads
+.TP
+trim:
+ Trim corrected reads
+.TP
+assemble:
+ Generate contigs
+.TP
+config:
+ Generate default config file
+
+
=====================================
debian/mans/mecat2pcan.1
=====================================
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH MECAT2PCAN "1" "July 2020" "mecat2pcan" "User Commands"
+.SH NAME
+mecat2pcan \- Partition consensus hits into smaller parts
+.SH SYNOPSIS
+mecat2pcan [\fI\,options\/\fR] \fI\,seqdb_dir \/\fR \fI\,pcan_dir \/\fR \fI\,cns_hits\/\fR
+.SH DESCRIPTION
+Command line tool to partition consensus hits into small parts
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-p\fR <Integer, >0>
+.IP
+Number of reads in each part
+Default = '100000'
+.HP
+\fB\-k\fR <Integer, >0>
+.IP
+Number of parts processed at each round
+(If <0, then it will be set to system limit value)
+Default = '100'
+.HP
+\fB\-t\fR <Integer, >0>
+.IP
+Number of CPU threads
+Default = '1'
+
=====================================
debian/mecat2.manpages
=====================================
@@ -0,0 +1 @@
+debian/mans/*.1
View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe
--
View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe
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