[med-svn] [paleomix] 05/08: Manual edits of auto generated manpages

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 13c0a6e0ce36ccad6fa3bc12b107b89112f1a8ba
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 23 09:57:32 2017 +0100

    Manual edits of auto generated manpages
---
 debian/mans/bam_pipeline.1        | 57 +++++++++++++++++++--------
 debian/mans/bam_rmdup_collapsed.1 | 13 +++++--
 debian/mans/conv_gtf_to_bed.1     | 28 ++++++++++++--
 debian/mans/paleomix.1            | 75 +++++++++++++++++-------------------
 debian/mans/phylo_pipeline.1      | 81 ++++++++++++++++++++++++---------------
 debian/mans/trim_pipeline.1       | 57 +++++++++++++++++++--------
 6 files changed, 204 insertions(+), 107 deletions(-)

diff --git a/debian/mans/bam_pipeline.1 b/debian/mans/bam_pipeline.1
index c924397..7c43451 100644
--- a/debian/mans/bam_pipeline.1
+++ b/debian/mans/bam_pipeline.1
@@ -1,22 +1,49 @@
-.\" 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>
+bam_pipeline \- BAM pipeline of PALEOMIX suite
+.SH SYNOPSIS
+.B bam_pipeline
+\fR[\fIoptions\/\fR]
 .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.
+The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+pipeline processes de-multiplexed reads from one or more samples,
+through sequence processing and alignment, to generate BAM alignment
+files useful in downstream analyses; the Phylogenetic pipeline carries
+out genotyping and phylogenetic inference on BAM alignment files, either
+produced using the BAM pipeline or generated elsewhere; and the Zonkey
+pipeline carries out a suite of analyses on low coverage equine
+alignments, in order to detect the presence of F1-hybrids in
+archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+analysis of the extracts.
+.P
+The pipelines have been designed with ancient DNA (aDNA) in mind, and
+includes several features especially useful for the analyses of ancient
+samples, but can all be for the processing of modern samples, in order
+to ensure consistent data processing.
+.P
+\fBbam_pipeline\fR is the BAM pipeline of paleomix(1).
+.SH OPTIONS
 .TP
-\fB\-\-\fR bam_pipeline dryrun [...]   \fB\-\-\fR Perform dry run of pipeline on provided makefiles.
+bam_pipeline help
+Display this message
+.TP
+bam_pipeline example [...]
+Create example project in folder.
+.TP
+bam_pipeline makefile [...]
+Print makefile template.
+.TP
+bam_pipeline dryrun [...]
+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.
+.TP
+bam_pipeline run [...]
+Run pipeline on provided makefiles.
+.TP
+bam_pipeline remap [...]
+Re\-map hits from previous alignment.
+.SH SEE ALSO
+paleomix(1)
 .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
index 7dde7c0..005b6b8 100644
--- a/debian/mans/bam_rmdup_collapsed.1
+++ b/debian/mans/bam_rmdup_collapsed.1
@@ -1,10 +1,10 @@
-.\" 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>
+bam_rmdup_collapsed \- filter BAM file for PCR duplicates
+.SH SYNOPSIS
+.B paleomix rmdup_collapsed
+[options] < sorted.bam > out.bam
 .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
@@ -18,6 +18,9 @@ using the BAM record flags, are not filtered, but simply written to the output.
 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.
+.PP
+This program is part of the paleomix(1) suite.
+.SH OPTIONS
 .SS "positional arguments:"
 .TP
 input
@@ -35,5 +38,7 @@ are only flagged (flag = 0x400).
 Seed used for randomly selecting representative reads
 when no reads have quality scores assigned[default:
 initialized using system time].
+.SH SEE ALSO
+paleomix(1)
 .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
index 8a77f43..9558d38 100644
--- a/debian/mans/conv_gtf_to_bed.1
+++ b/debian/mans/conv_gtf_to_bed.1
@@ -1,9 +1,29 @@
-.\" 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>
+conv_gtf_to_bed \- legacy script for invoking the PALEOMIX command "gtf_to_bed"
+.SH SYNOPSIS
+.B paleomix gtf_to_bed
+[options] in.gtf out_prefix [in.scaffolds]
 .SH DESCRIPTION
-usage: paleomix gtf_to_bed [options] in.gtf out_prefix [in.scaffolds]
+The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+pipeline processes de-multiplexed reads from one or more samples,
+through sequence processing and alignment, to generate BAM alignment
+files useful in downstream analyses; the Phylogenetic pipeline carries
+out genotyping and phylogenetic inference on BAM alignment files, either
+produced using the BAM pipeline or generated elsewhere; and the Zonkey
+pipeline carries out a suite of analyses on low coverage equine
+alignments, in order to detect the presence of F1-hybrids in
+archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+analysis of the extracts.
+.P
+The pipelines have been designed with ancient DNA (aDNA) in mind, and
+includes several features especially useful for the analyses of ancient
+samples, but can all be for the processing of modern samples, in order
+to ensure consistent data processing.
+.P
+\fBconv_gtf_to_bed\fR is a legacy script for invoking the paleomix(1) command "gtf_to_bed"
+.SH OPTIONS
 .SS "positional arguments:"
 .TP
 INPUT.gtf
@@ -33,5 +53,7 @@ even if the the length of the CDS is not divisible by
 \fB\-\-contig\-prefix\fR CONTIG_PREFIX
 Add prefix to contig names (e.g. 'chr') [default: no
 prefix].
+.SH SEE ALSO
+paleomix(1)
 .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
index 8720368..bb1683d 100644
--- a/debian/mans/paleomix.1
+++ b/debian/mans/paleomix.1
@@ -1,93 +1,90 @@
-.\" 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>
+paleomix \- pipelines and tools for HTS data analyses
 .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:"
+The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+pipeline processes de-multiplexed reads from one or more samples,
+through sequence processing and alignment, to generate BAM alignment
+files useful in downstream analyses; the Phylogenetic pipeline carries
+out genotyping and phylogenetic inference on BAM alignment files, either
+produced using the BAM pipeline or generated elsewhere; and the Zonkey
+pipeline carries out a suite of analyses on low coverage equine
+alignments, in order to detect the presence of F1-hybrids in
+archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+analysis of the extracts.
+.P
+The pipelines have been designed with ancient DNA (aDNA) in mind, and
+includes several features especially useful for the analyses of ancient
+samples, but can all be for the processing of modern samples, in order
+to ensure consistent data processing.
+.SH OPTIONS
+.SS Pipelines
 .TP
 paleomix bam_pipeline
-\fB\-\-\fR Pipeline for trimming and mapping of NGS reads.
+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.
+Equivalent to 'bam_pipeline', but only runs the trimming steps.
 .TP
 paleomix phylo_pipeline
-\fB\-\-\fR Pipeline for genotyping and phylogenetic
-.IP
-inference from BAMs.
+Pipeline for genotyping and phylogenetic inference from BAMs.
 .TP
 paleomix zonkey
-\fB\-\-\fR Pipeline for detecting F1 (equine) hybrids.
+Pipeline for detecting F1 (equine) hybrids.
 .SS "BAM/SAM tools:"
 .TP
 paleomix cleanup
-\fB\-\-\fR Reads SAM file from STDIN, and outputs sorted,
-.TP
+Reads SAM file from STDIN, and outputs sorted,
 tagged, and filter BAM, for which NM and MD
 tags have been updated.
 .TP
 paleomix coverage
-\fB\-\-\fR Calculate coverage across reference sequences
-.IP
+Calculate coverage across reference sequences
 or regions of interest.
 .TP
 paleomix depths
-\fB\-\-\fR Calculate depth histograms across reference
-.IP
-sequences or regions of interest.
+Calculate depth histograms across reference sequences or regions of interest.
 .TP
 paleomix duphist
-\fB\-\-\fR Generates PCR duplicate histogram; used with
-.IP
-the 'Preseq' tool.
+Generates PCR duplicate histogram; used with the 'Preseq' tool.
 .TP
 paleomix rmdup_collapsed
-\fB\-\-\fR Filters PCR duplicates for collapsed pairedended reads generated by the AdapterRemoval
-.IP
-tool.
+Filters PCR duplicates for collapsed pairedended reads generated by the AdapterRemoval tool.
 .SS "VCF/GTF/BED/Pileup tools:"
 .TP
 paleomix genotype
-\fB\-\-\fR Creates bgzipped VCF for a set of (sparse) BED
-.TP
+Creates bgzipped VCF for a set of (sparse) BED
 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
+Convert GTF file to BED files grouped by
 feature (coding, RNA, etc).
 .TP
 paleomix sample_pileup
-\fB\-\-\fR Randomly sample sites in a pileup to generate a
-.IP
+Randomly sample sites in a pileup to generate a
 FASTA sequence.
 .TP
 paleomix vcf_filter
-\fB\-\-\fR Quality filters for VCF records, similar to
-.IP
+Quality filters for VCF records, similar to
 \&'vcfutils.pl varFilter'.
 .TP
 paleomix vcf_to_fasta
-\fB\-\-\fR Create most likely FASTA sequence from tabixindexed VCF file.
+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
+Generalized cat command for gz, bz2 and
 uncompressed files.
-.PP
+.SH AUTHOR
 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
+.P
 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
index c3d2998..7eb8d12 100644
--- a/debian/mans/phylo_pipeline.1
+++ b/debian/mans/phylo_pipeline.1
@@ -1,25 +1,49 @@
-.\" 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>
+phylo_pipeline \- Phylo Pipeline of PALEOMIX suite
 .SH SYNOPSIS
-.B paleomix
-\fI\,phylo_pipeline <command> \/\fR[\fI\,options\/\fR] [\fI\,makefiles\/\fR]
+.B paleomix 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.
+The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+pipeline processes de-multiplexed reads from one or more samples,
+through sequence processing and alignment, to generate BAM alignment
+files useful in downstream analyses; the Phylogenetic pipeline carries
+out genotyping and phylogenetic inference on BAM alignment files, either
+produced using the BAM pipeline or generated elsewhere; and the Zonkey
+pipeline carries out a suite of analyses on low coverage equine
+alignments, in order to detect the presence of F1-hybrids in
+archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+analysis of the extracts.
+.P
+The pipelines have been designed with ancient DNA (aDNA) in mind, and
+includes several features especially useful for the analyses of ancient
+samples, but can all be for the processing of modern samples, in order
+to ensure consistent data processing.
+.P
+\fBphylo_pipeline\fR is the phylo pipeline of paleomix(1).
 .SH OPTIONS
+.SS Commands
+.TP
+phylo_pipeline help
+Display this message.
+.TP
+phylo_pipeline example [...]
+Copy example project to folder.
+.TP
+phylo_pipeline makefile
+Print makefile template.
+.TP
+phylo_pipeline genotype [...]
+Carry out genotyping according to makefile.
+.TP
+phylo_pipeline msa [...]
+Carry out multiple sequence alignment.
+.TP
+phylo_pipeline phylogeny
+Carry out phylogenetic inference.
+.SS Optional arguments
 .TP
 \fB\-\-version\fR
 show program's version number and exit
@@ -29,8 +53,7 @@ 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:
+.SS Progress reporting
 .TP
 \fB\-\-progress\-ui\fR=\fI\,PROGRESS_UI\/\fR
 Select method for displaying the progress of the
@@ -44,8 +67,7 @@ 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:
+.SS Logging
 .TP
 \fB\-\-log\-file\fR=\fI\,LOG_FILE\/\fR
 Create the specified log\-file and write any messages
@@ -57,8 +79,7 @@ when messages are logged
 Log messages to log\-file at and above the specified
 level; one of 'info', 'warning', 'error', or 'debug'
 [warning]
-.IP
-Scheduling:
+.SS Scheduling
 .TP
 \fB\-\-samtools\-max\-threads\fR=\fI\,SAMTOOLS_MAX_THREADS\/\fR
 Maximum number of threads to use when genotyping or
@@ -74,8 +95,7 @@ Maximum number of threads to use in total [4]
 \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:
+.SS Required paths:
 .TP
 \fB\-\-temp\-root\fR=\fI\,TEMP_ROOT\/\fR
 Location for temporary files and folders
@@ -97,8 +117,7 @@ Location of reference sequences (FASTAs)
 .TP
 \fB\-\-destination\fR=\fI\,DESTINATION\/\fR
 The destination folder for result files [./results]
-.IP
-Files and executables:
+.SS Files and executables:
 .TP
 \fB\-\-list\-input\-files\fR
 List all input files used by pipeline for the
@@ -112,11 +131,11 @@ makefile(s).
 \fB\-\-list\-executables\fR
 List all executables required by the pipeline, with
 version requirements (if any).
-.IP
-Config files:
+.SS Config files:
 .TP
 \fB\-\-write\-config\-file\fR
-Write config using current settings to
-/home/tillea/.paleomix/phylo_pipeline.ini
+Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini
+.SH SEE ALSO
+paleomix(1)
 .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
index fd46ae9..8c38469 100644
--- a/debian/mans/trim_pipeline.1
+++ b/debian/mans/trim_pipeline.1
@@ -1,22 +1,49 @@
-.\" 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>
+trim_pipeline \- trim pipeline of PALEOMIX suite
+.SH SYNOPSIS
+.B trim_pipeline
+\fR[\fIoptions\/\fR]
 .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.
+The PALEOMIX pipelines are a set of pipelines and tools designed to aid
+the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
+pipeline processes de-multiplexed reads from one or more samples,
+through sequence processing and alignment, to generate BAM alignment
+files useful in downstream analyses; the Phylogenetic pipeline carries
+out genotyping and phylogenetic inference on BAM alignment files, either
+produced using the BAM pipeline or generated elsewhere; and the Zonkey
+pipeline carries out a suite of analyses on low coverage equine
+alignments, in order to detect the presence of F1-hybrids in
+archaeological assemblages. In addition, PALEOMIX aids in metagenomic
+analysis of the extracts.
+.P
+The pipelines have been designed with ancient DNA (aDNA) in mind, and
+includes several features especially useful for the analyses of ancient
+samples, but can all be for the processing of modern samples, in order
+to ensure consistent data processing.
+.P
+\fBtrim_pipeline\fR is the trim pipeline of paleomix(1).
+.SH OPTIONS
 .TP
-\fB\-\-\fR trim_pipeline dryrun [...]   \fB\-\-\fR Perform dry run of pipeline on provided makefiles.
+trim_pipeline help
+Display this message
+.TP
+trim_pipeline example [...]
+Create example project in folder.
+.TP
+trim_pipeline makefile [...]
+Print makefile template.
+.TP
+trim_pipeline dryrun [...]
+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.
+.TP
+trim_pipeline run [...]
+Run pipeline on provided makefiles.
+.TP
+trim_pipeline remap [...]
+Re\-map hits from previous alignment.
+.SH SEE ALSO
+paleomix(1)
 .SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paleomix.git

