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commit 20ea2b8d7a5d095af7295209e93abff6edb17cee Author: Andreas Tille <[email protected]> Date: Thu Mar 31 09:44:11 2016 +0200 Add manpages --- debian/control | 1 + debian/manpages | 1 + debian/mans/surankco-feature.1 | 73 +++++++++++++++++++++++++++++++++++++++ debian/mans/surankco-prediction.1 | 29 ++++++++++++++++ debian/mans/surankco-score.1 | 45 ++++++++++++++++++++++++ debian/mans/surankco-training.1 | 41 ++++++++++++++++++++++ 6 files changed, 190 insertions(+) diff --git a/debian/control b/debian/control index e04c901..0165dac 100644 --- a/debian/control +++ b/debian/control @@ -18,6 +18,7 @@ Depends: ${java:Depends}, ${misc:Depends}, r-base-core, r-cran-mass, + r-cran-optparse, r-cran-randomforest Description: Supervised Ranking of Contigs in de novo Assemblies SuRankCo is a machine learning based software to score and rank 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/surankco-feature.1 b/debian/mans/surankco-feature.1 new file mode 100644 index 0000000..b7bf58f --- /dev/null +++ b/debian/mans/surankco-feature.1 @@ -0,0 +1,73 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. +.TH SURANKCO-FEATURE "1" "March 2016" "surankco-feature 0.0.r5" "User Commands" +.SH NAME +surankco-feature \- feature generation from contigs and corresponding reads +.SH SYNOPSIS +.B surankco-feature +[\fI\,options\/\fR] +.SH DESCRIPTION +Feature generation from contigs (ACE format) and corresponding reads (QUAL or FASTQ format). +.SH OPTIONS +.HP +\fB\-a\fR ASSEMBLIES, \fB\-\-assemblies\fR=\fI\,ASSEMBLIES\/\fR +.IP +Indicate a list of assembly files (comma separated), correct +suffixes are mandatory (e.g. ".ace") +.HP +\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR +.IP +Indicate a directory containing assembly files with indicated +format (default: ace, see parameter \fB\-f\fR) +.HP +\fB\-f\fR ASSEMBLY.FORMAT, \fB\-\-assembly\fR.format=ASSEMBLY.FORMAT +.IP +Indicate assembly/contig format (resp. suffix), +either "ace" (default) or "contigs.fasta" +.HP +\fB\-r\fR READ.QUALITY.FORMAT, \fB\-\-read\fR.quality.format=READ.QUALITY.FORMAT +.IP +Indicate the read quality format: qual, qua or fastq for ACE +(default="qual") resp. sam or bam for contigs.fasta (default="sam") +.HP +\fB\-q\fR FASTQ.VERSION, \fB\-\-fastq\fR.version=FASTQ.VERSION +.IP +Indicate the fastq version: auto, sanger, solexa, illumina13, +illumina15, illumina18 (default). Only needed for ACE assemblies. +.HP +\fB\-s\fR SPLIT.REGEX, \fB\-\-split\fR.regex=SPLIT.REGEX +.IP +Indicate a regular expression to cutoff read names (e.g. if +modified by the assembler). Only needed for ACE assemblies. +Note, if a backslash "\e" is needed use "\e\e\e\e"! +.HP +\fB\-t\fR THREADS, \fB\-\-threads\fR=\fI\,THREADS\/\fR +.IP +Indicate a number of cores or threads to use. Might speed up +some parallelized operations (default: 1) +.HP +\fB\-m\fR MEMORY, \fB\-\-memory\fR=\fI\,MEMORY\/\fR +.IP +Indicate the maximum memory usage (in Gb) of Javas virtual +machine (default: 32). Try to increase if big data sets report +heap space problems. +.HP +\fB\-k\fR, \fB\-\-kmer\fR.features +.IP +Indicates whether k\-mer features should be computed +(experimental, very long runtime) or not (default) +.HP +\fB\-g\fR EXPECTED.GENOME.SIZE, \fB\-\-expected\fR.genome.size=EXPECTED.GENOME.SIZE +.IP +Indicate a list of expected genome sizes (comma separated) or +one value for all assemblies. Default is 0, which will estimate +the genome sizes as sum of contig lengths. +.HP +\fB\-c\fR CONTIG.SIZE.FILTER, \fB\-\-contig\fR.size.filter=CONTIG.SIZE.FILTER +.IP +Indicate a minimum contig size. Default: 0 +.HP +\fB\-h\fR, \fB\-\-help\fR +.IP +Show this help message and exit +.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/surankco-prediction.1 b/debian/mans/surankco-prediction.1 new file mode 100644 index 0000000..60289ab --- /dev/null +++ b/debian/mans/surankco-prediction.1 @@ -0,0 +1,29 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. +.TH SURANKCO-PREDICTION "1" "March 2016" "surankco-prediction 0.0.r5" "User Commands" +.SH NAME +surankco-prediction \- prediction of scores and ranking of contigs using trained random forests and contig features +.SH SYNOPSIS +.B surankco-prediction +[\fI\,options\/\fR] +.SH DESCRIPTION +Prediction of scores and ranking of contigs using trained random forests created by surankco-training(1) and contig features from surankco-feature(1). +.SH OPTIONS +.HP +\fB\-f\fR FEATURES, \fB\-\-features\fR=\fI\,FEATURES\/\fR +.IP +Indicate one surankco feature file, a correct suffixe is +mandatory ("*.features.txt") +.HP +\fB\-r\fR RANDOM.FORESTS, \fB\-\-random\fR.forests=RANDOM.FORESTS +.IP +Indicate a surankco random forests file ("*.RData") +.HP +\fB\-o\fR OUTPUT.FILENAME, \fB\-\-output\fR.filename=OUTPUT.FILENAME +.IP +Indicate a name for the final results file +.HP +\fB\-h\fR, \fB\-\-help\fR +.IP +Show this help message and exit +.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/surankco-score.1 b/debian/mans/surankco-score.1 new file mode 100644 index 0000000..3631df3 --- /dev/null +++ b/debian/mans/surankco-score.1 @@ -0,0 +1,45 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. +.TH SURANKCO-SCORE "1" "March 2016" "surankco-score 0.0.r5" "User Commands" +.SH NAME +surankco-score \- alignment of contigs and reference genomes and score calculation +.SH SYNOPSIS +.B surankco-score +[\fI\,options\/\fR] +.SH DESCRIPTION +Alignment of contigs (FASTA format) and reference genomes (FASTA format) and score calculation +.SH OPTIONS +.HP +\fB\-a\fR ASSEMBLIES, \fB\-\-assemblies\fR=\fI\,ASSEMBLIES\/\fR +.IP +Indicate a list of assembly files (comma separated), correct +suffixes are mandatory (default "*.contigs.fasta") +.HP +\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR +.IP +Indicate a directory containing assembly files with indicated +format (e.g. "*.contigs.fasta") +.HP +\fB\-f\fR ASSEMBLY.SUFFIX, \fB\-\-assembly\fR.suffix=ASSEMBLY.SUFFIX +.IP +Indicate assembly format/suffix, default="contigs.fasta" +.HP +\fB\-r\fR REFERENCE.SUFFIX, \fB\-\-reference\fR.suffix=REFERENCE.SUFFIX +.IP +Indicate the reference format/suffix, default="ref.fasta" +.HP +\fB\-p\fR PDF.HISTOGRAMS, \fB\-\-pdf\fR.histograms=PDF.HISTOGRAMS +.IP +Indicate a name for the score histogram pdf +(default = "surankco_score_histograms.pdf") +.HP +\fB\-m\fR MEMORY, \fB\-\-memory\fR=\fI\,MEMORY\/\fR +.IP +Indicate the maximum memory usage (in Gb) of Javas virtual +machine (default: 32). Try to increase if big data sets report +heap space problems. +.HP +\fB\-h\fR, \fB\-\-help\fR +.IP +Show this help message and exit +.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/surankco-training.1 b/debian/mans/surankco-training.1 new file mode 100644 index 0000000..9867d0f --- /dev/null +++ b/debian/mans/surankco-training.1 @@ -0,0 +1,41 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. +.TH SURANKCO-TRAINING "1" "March 2016" "surankco-training 0.0.r5" "User Commands" +.SH NAME +surankco-training \- training of random forest using contig features and contig scores +.SH SYNOPSIS +.B surankco-training +[\fI\,options\/\fR] +.SH DESCRIPTION +Training of random forest using contig features from surankco-feature(1) and contig scores from surankco-score(1). +.SH OPTIONS +.HP +\fB\-f\fR FEATURES, \fB\-\-features\fR=\fI\,FEATURES\/\fR +.IP +Indicate a list of surankco feature files (comma separated), +correct suffixes are mandatory ("*.features.txt") +.HP +\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR +.IP +Indicate a directory containing surankco feature files +("*.features.txt") +.HP +\fB\-o\fR OUTPUT.FILENAME, \fB\-\-output\fR.filename=OUTPUT.FILENAME +.IP +Indicate a name for the export of the random forest classifiers +(default = "surankco_rfs.RData") +.HP +\fB\-e\fR EXPONENTIAL.QUANTILE, \fB\-\-exponential\fR.quantile=EXPONENTIAL.QUANTILE +.IP +Indicate an exponential distribution quantile to divide scores +(default: 0.25) +.HP +\fB\-m\fR MANUAL.THRESHOLDS, \fB\-\-manual\fR.thresholds=MANUAL.THRESHOLDS +.IP +Indicate manual thresholds instead of quantiles, one per score +each (comma separated) in the same order as in the score file +.HP +\fB\-h\fR, \fB\-\-help\fR +.IP +Show this help message and exit +.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/surankco.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
