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commit 1e49ab928146c86c3e43a4c95fb79bfb4533eaa7 Author: Andreas Tille <[email protected]> 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paleomix.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
