[med-svn] [surankco] 01/02: Add manpages
Andreas Tille
tille at debian.org
Thu Mar 31 11:41:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository surankco.
commit 20ea2b8d7a5d095af7295209e93abff6edb17cee
Author: Andreas Tille <tille at debian.org>
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.
--
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