[med-svn] [paleomix] 04/08: Manpages
Andreas Tille
tille at debian.org
Thu Mar 9 07:45:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository paleomix.
commit 1e49ab928146c86c3e43a4c95fb79bfb4533eaa7
Author: Andreas Tille <tille at debian.org>
Date: Thu Feb 23 09:06:14 2017 +0100
Manpages
---
debian/createmanpages | 52 ++++++++++++++++
debian/manpages | 1 +
debian/mans/bam_pipeline.1 | 22 +++++++
debian/mans/bam_rmdup_collapsed.1 | 39 ++++++++++++
debian/mans/conv_gtf_to_bed.1 | 37 ++++++++++++
debian/mans/paleomix.1 | 93 +++++++++++++++++++++++++++++
debian/mans/phylo_pipeline.1 | 122 ++++++++++++++++++++++++++++++++++++++
debian/mans/trim_pipeline.1 | 22 +++++++
8 files changed, 388 insertions(+)
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..31ff375
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,52 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=paleomix
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bam_pipeline
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bam_rmdup_collapsed
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=conv_gtf_to_bed
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=phylo_pipeline
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=trim_pipeline
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/bam_pipeline.1 b/debian/mans/bam_pipeline.1
new file mode 100644
index 0000000..c924397
--- /dev/null
+++ b/debian/mans/bam_pipeline.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH BAM_PIPELINE "1" "February 2017" "bam_pipeline 1.2.7" "User Commands"
+.SH NAME
+bam_pipeline \- <optional description of the program>
+.SH DESCRIPTION
+BAM Pipeline v1.2.7
+.SS "Usage:"
+.HP
+\fB\-\-\fR bam_pipeline help \fB\-\-\fR Display this message
+.HP
+\fB\-\-\fR bam_pipeline example [...] \fB\-\-\fR Create example project in folder.
+.HP
+\fB\-\-\fR bam_pipeline makefile [...] \fB\-\-\fR Print makefile template.
+.TP
+\fB\-\-\fR bam_pipeline dryrun [...] \fB\-\-\fR Perform dry run of pipeline on provided makefiles.
+Equivalent to 'bam_pipeline run \fB\-\-dry\-run\fR [...]'.
+.HP
+\fB\-\-\fR bam_pipeline run [...] \fB\-\-\fR Run pipeline on provided makefiles.
+.HP
+\fB\-\-\fR bam_pipeline remap [...] \fB\-\-\fR Re\-map hits from previous alignment.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/bam_rmdup_collapsed.1 b/debian/mans/bam_rmdup_collapsed.1
new file mode 100644
index 0000000..7dde7c0
--- /dev/null
+++ b/debian/mans/bam_rmdup_collapsed.1
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH BAM_RMDUP_COLLAPSED "1" "February 2017" "bam_rmdup_collapsed 1.2.7" "User Commands"
+.SH NAME
+bam_rmdup_collapsed \- <optional description of the program>
+.SH DESCRIPTION
+usage: paleomix rmdup_collapsed [options] < sorted.bam > out.bam
+.PP
+The rmdup_collapsed filters a BAM file for PCR duplicates unpaired reads under
+the assumption that any unpaired read have been generated by the merging of
+overlapping paired\-end reads, and thereby represent the complete template
+sequence. PCR duplicates are therefore detected based on both the 5' and 3'
+alignment coordinate.
+.PP
+Paired reads (0x1), unmapped reads (0x4), secondary alignments (0x100),
+reads that failed QC (0x200), and chimeric alignments (0x800), as identified
+using the BAM record flags, are not filtered, but simply written to the output.
+.PP
+By default, filtered reads are flagged using the "duplicate" flag (0x400), and
+written to the output. Use the \fB\-\-remove\-duplicates\fR command\-line option to
+instead remove these records from the output.
+.SS "positional arguments:"
+.TP
+input
+BAM file; if not set, input is read from STDIN.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-remove\-duplicates\fR
+Remove duplicates from output; by default duplicates
+are only flagged (flag = 0x400).
+.TP
+\fB\-\-seed\fR SEED
+Seed used for randomly selecting representative reads
+when no reads have quality scores assigned[default:
+initialized using system time].
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/conv_gtf_to_bed.1 b/debian/mans/conv_gtf_to_bed.1
new file mode 100644
index 0000000..8a77f43
--- /dev/null
+++ b/debian/mans/conv_gtf_to_bed.1
@@ -0,0 +1,37 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH CONV_GTF_TO_BED "1" "February 2017" "conv_gtf_to_bed 1.2.7" "User Commands"
+.SH NAME
+conv_gtf_to_bed \- <optional description of the program>
+.SH DESCRIPTION
+usage: paleomix gtf_to_bed [options] in.gtf out_prefix [in.scaffolds]
+.SS "positional arguments:"
+.TP
+INPUT.gtf
+Input file in GTF format.
+.TP
+OUTPUT_PREFIX
+Prefix of output files.
+.TP
+SCAFFOLDS
+Mapping of scaffolds to contig positions; e.g. mapping
+individual Un* scaffolds onto chrUn.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-keep\-all\-transcripts\fR
+Include all transcripts in the output BED files, not
+just the longest transcript of each gene [default:
+off]
+.TP
+\fB\-\-keep\-malformed\-proteins\fR
+Include transcripts of protein\-coding in the output,
+even if the the length of the CDS is not divisible by
+3 [default: off]
+.TP
+\fB\-\-contig\-prefix\fR CONTIG_PREFIX
+Add prefix to contig names (e.g. 'chr') [default: no
+prefix].
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/paleomix.1 b/debian/mans/paleomix.1
new file mode 100644
index 0000000..8720368
--- /dev/null
+++ b/debian/mans/paleomix.1
@@ -0,0 +1,93 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PALEOMIX "1" "February 2017" "paleomix 1.2.7" "User Commands"
+.SH NAME
+paleomix \- <optional description of the program>
+.SH SYNOPSIS
+.B paleomix
+\fI\,<command> \/\fR[\fI\,options\/\fR]
+.SH DESCRIPTION
+PALEOMIX \- pipelines and tools for NGS data analyses.
+Version: 1.2.7
+.SS "Pipelines:"
+.TP
+paleomix bam_pipeline
+\fB\-\-\fR Pipeline for trimming and mapping of NGS reads.
+.TP
+paleomix trim_pipeline
+\fB\-\-\fR Equivalent to 'bam_pipeline', but only runs the
+.IP
+trimming steps.
+.TP
+paleomix phylo_pipeline
+\fB\-\-\fR Pipeline for genotyping and phylogenetic
+.IP
+inference from BAMs.
+.TP
+paleomix zonkey
+\fB\-\-\fR Pipeline for detecting F1 (equine) hybrids.
+.SS "BAM/SAM tools:"
+.TP
+paleomix cleanup
+\fB\-\-\fR Reads SAM file from STDIN, and outputs sorted,
+.TP
+tagged, and filter BAM, for which NM and MD
+tags have been updated.
+.TP
+paleomix coverage
+\fB\-\-\fR Calculate coverage across reference sequences
+.IP
+or regions of interest.
+.TP
+paleomix depths
+\fB\-\-\fR Calculate depth histograms across reference
+.IP
+sequences or regions of interest.
+.TP
+paleomix duphist
+\fB\-\-\fR Generates PCR duplicate histogram; used with
+.IP
+the 'Preseq' tool.
+.TP
+paleomix rmdup_collapsed
+\fB\-\-\fR Filters PCR duplicates for collapsed pairedended reads generated by the AdapterRemoval
+.IP
+tool.
+.SS "VCF/GTF/BED/Pileup tools:"
+.TP
+paleomix genotype
+\fB\-\-\fR Creates bgzipped VCF for a set of (sparse) BED
+.TP
+regions, or for entire chromosomes / contigs
+using SAMTools / BCFTools.
+.TP
+paleomix gtf_to_bed
+\fB\-\-\fR Convert GTF file to BED files grouped by
+.IP
+feature (coding, RNA, etc).
+.TP
+paleomix sample_pileup
+\fB\-\-\fR Randomly sample sites in a pileup to generate a
+.IP
+FASTA sequence.
+.TP
+paleomix vcf_filter
+\fB\-\-\fR Quality filters for VCF records, similar to
+.IP
+\&'vcfutils.pl varFilter'.
+.TP
+paleomix vcf_to_fasta
+\fB\-\-\fR Create most likely FASTA sequence from tabixindexed VCF file.
+.SS "Misc tools:"
+.TP
+paleomix cat
+\fB\-\-\fR Generalized cat command for gz, bz2 and
+.IP
+uncompressed files.
+.PP
+If you make use of PALEOMIX in your work, please cite
+.IP
+Schubert et al, "Characterization of ancient and modern genomes by SNP
+detection and phylogenomic and metagenomic analysis using PALEOMIX".
+Nature Protocols. 2014 May; 9(5): 1056\-82. doi: 10.1038/nprot.2014.063
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/phylo_pipeline.1 b/debian/mans/phylo_pipeline.1
new file mode 100644
index 0000000..c3d2998
--- /dev/null
+++ b/debian/mans/phylo_pipeline.1
@@ -0,0 +1,122 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PHYLO_PIPELINE "1" "February 2017" "phylo_pipeline 1.2.7" "User Commands"
+.SH NAME
+phylo_pipeline \- <optional description of the program>
+.SH SYNOPSIS
+.B paleomix
+\fI\,phylo_pipeline <command> \/\fR[\fI\,options\/\fR] [\fI\,makefiles\/\fR]
+.SH DESCRIPTION
+.SS "Commands:"
+.HP
+\fB\-\-\fR phylo_pipeline help \fB\-\-\fR Display this message.
+.HP
+\fB\-\-\fR phylo_pipeline example [...] \fB\-\-\fR Copy example project to folder.
+.HP
+\fB\-\-\fR phylo_pipeline makefile \fB\-\-\fR Print makefile template.
+.HP
+\fB\-\-\fR phylo_pipeline genotype [...] \fB\-\-\fR Carry out genotyping according to makefile.
+.HP
+\fB\-\-\fR phylo_pipeline msa [...] \fB\-\-\fR Carry out multiple sequence alignment.
+.HP
+\fB\-\-\fR phylo_pipeline phylogeny [...] \fB\-\-\fR Carry out phylogenetic inference.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-to\-dot\-file\fR=\fI\,DOT_FILE\/\fR
+Write dependency tree to the specified dot\-file.
+.IP
+Progress reporting:
+.TP
+\fB\-\-progress\-ui\fR=\fI\,PROGRESS_UI\/\fR
+Select method for displaying the progress of the
+pipeline: 'running' = Display only currently running
+nodes; 'progress' = Display changes in state;
+\&'summary'; one\-line summary only. [Default is
+\&'running']
+.TP
+\fB\-\-ui\-colors\fR=\fI\,UI_COLORS\/\fR
+Enable, disable, or force the use of color codes when
+printing the command\-line UI. Unless forced, colors
+will only be printed if STDOUT is a TTY [Default is
+\&'on']
+.IP
+Logging:
+.TP
+\fB\-\-log\-file\fR=\fI\,LOG_FILE\/\fR
+Create the specified log\-file and write any messages
+to this file. By default, a log\-file will be generated
+in the folder specified using \fB\-\-temp\-root\fR, but only
+when messages are logged
+.TP
+\fB\-\-log\-level\fR=\fI\,LOG_LEVEL\/\fR
+Log messages to log\-file at and above the specified
+level; one of 'info', 'warning', 'error', or 'debug'
+[warning]
+.IP
+Scheduling:
+.TP
+\fB\-\-samtools\-max\-threads\fR=\fI\,SAMTOOLS_MAX_THREADS\/\fR
+Maximum number of threads to use when genotyping or
+building pileups [1]
+.TP
+\fB\-\-examl\-max\-threads\fR=\fI\,EXAML_MAX_THREADS\/\fR
+Maximum number of threads to use for each instance of
+ExaML [1]
+.TP
+\fB\-\-max\-threads\fR=\fI\,MAX_THREADS\/\fR
+Maximum number of threads to use in total [4]
+.TP
+\fB\-\-dry\-run\fR
+If passed, only a dry\-run in performed, the dependency
+tree is printed, and no tasks are executed.
+.IP
+Required paths:
+.TP
+\fB\-\-temp\-root\fR=\fI\,TEMP_ROOT\/\fR
+Location for temporary files and folders
+[/tmp/tillea/phylo_pipeline]
+.TP
+\fB\-\-samples\-root\fR=\fI\,SAMPLES_ROOT\/\fR
+Location of BAM files for each sample [./data/samples]
+.TP
+\fB\-\-regions\-root\fR=\fI\,REGIONS_ROOT\/\fR
+Location of BED files containing regions of interest
+[./data/regions]
+.TP
+\fB\-\-prefix\-root\fR=\fI\,PREFIX_ROOT\/\fR
+Location of prefixes (FASTAs) [./data/prefixes]
+.TP
+\fB\-\-refseq\-root\fR=\fI\,REFSEQ_ROOT\/\fR
+Location of reference sequences (FASTAs)
+[./data/refseqs]
+.TP
+\fB\-\-destination\fR=\fI\,DESTINATION\/\fR
+The destination folder for result files [./results]
+.IP
+Files and executables:
+.TP
+\fB\-\-list\-input\-files\fR
+List all input files used by pipeline for the
+makefile(s), excluding any generated by the pipeline
+itself.
+.TP
+\fB\-\-list\-output\-files\fR
+List all output files generated by pipeline for the
+makefile(s).
+.TP
+\fB\-\-list\-executables\fR
+List all executables required by the pipeline, with
+version requirements (if any).
+.IP
+Config files:
+.TP
+\fB\-\-write\-config\-file\fR
+Write config using current settings to
+/home/tillea/.paleomix/phylo_pipeline.ini
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/trim_pipeline.1 b/debian/mans/trim_pipeline.1
new file mode 100644
index 0000000..fd46ae9
--- /dev/null
+++ b/debian/mans/trim_pipeline.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH TRIM_PIPELINE "1" "February 2017" "trim_pipeline 1.2.7" "User Commands"
+.SH NAME
+trim_pipeline \- <optional description of the program>
+.SH DESCRIPTION
+BAM Pipeline v1.2.7
+.SS "Usage:"
+.HP
+\fB\-\-\fR trim_pipeline help \fB\-\-\fR Display this message
+.HP
+\fB\-\-\fR trim_pipeline example [...] \fB\-\-\fR Create example project in folder.
+.HP
+\fB\-\-\fR trim_pipeline makefile [...] \fB\-\-\fR Print makefile template.
+.TP
+\fB\-\-\fR trim_pipeline dryrun [...] \fB\-\-\fR Perform dry run of pipeline on provided makefiles.
+Equivalent to 'bam_pipeline run \fB\-\-dry\-run\fR [...]'.
+.HP
+\fB\-\-\fR trim_pipeline run [...] \fB\-\-\fR Run pipeline on provided makefiles.
+.HP
+\fB\-\-\fR trim_pipeline remap [...] \fB\-\-\fR Re\-map hits from previous alignment.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
--
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