[med-svn] [giira] 01/01: Add manpage (based on help2man output)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository giira.

commit 10cfc6c73b05c47659cbe3edf6634f82e6c1b349
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 10 14:16:59 2014 +0100

    Add manpage (based on help2man output)
---
 debian/bin/giira      |  2 +-
 debian/createmanpages |  3 +++
 debian/giira.1        | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages       |  1 +
 4 files changed, 63 insertions(+), 1 deletion(-)

diff --git a/debian/bin/giira b/debian/bin/giira
index 2aefcd3..1ca09cf 100755
--- a/debian/bin/giira
+++ b/debian/bin/giira
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-java $JAVA_OPTS -jar /usr/share/java/`basename $0`.jar $@
+java $JAVA_OPTS -jar /usr/share/java/`basename $0`.jar -opti glpk $@
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..eaef2e4
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,3 @@
+help2man --no-info --no-discard-stderr \
+         --name='Gene Identification Incorporating RNA-Seq data and Ambiguous reads' \
+            --version-string="2014-02-10" giira > debian/giira.1
diff --git a/debian/giira.1 b/debian/giira.1
new file mode 100644
index 0000000..99fc9e5
--- /dev/null
+++ b/debian/giira.1
@@ -0,0 +1,58 @@
+.TH GIIRA "1" "February 2014" "giira 2014-02-10" "User Commands"
+.SH NAME
+giira \- Gene Identification Incorporating RNA-Seq data and Ambiguous reads
+.SH SYNOPSIS
+.B giira
+\fB\-iG\fR genomeFile.fasta \fB\-iR\fR rnaFile.fastq \fB\-libPath\fR
+.SH DESCRIPTION
+GIIRA (Gene Identification Incorporating RNA\-Seq data and Ambiguous reads) is a method to identify potential gene regions in a genome based on a RNA\-Seq mapping and incorporating ambiguously mapped reads.
+.SH OPTIONS
+.HP
+\fB\-h\fR : help text and exit
+.HP
+\fB\-iG\fR [pathToGenomes] : specify path to directory with genome files in fasta format
+.HP
+\fB\-iR\fR [pathToRna] : specify path to directory with rna read files in fastq format
+.HP
+\fB\-scripts\fR [absolutePath] : specify the absolute path to the directory containing the required helper scripts, DEFAULT: directory of GIIRA.jar
+.HP
+\fB\-out\fR [pathToResults] : specify the directory that shall contain the results files
+.HP
+\fB\-outName\fR [outputName] : specify desired name for output files, DEFAULT: genes
+.HP
+\fB\-haveSam\fR [samfileName]: if a sam file already exists, provide the name, else a mapping is performed. NOTE: the sam file has to be sorted according to read names!
+.HP
+\fB\-nT\fR [numberThreads] : specify the maximal number of threads that are allowed to be used, DEFAULT: 1
+.HP
+\fB\-mT\fR [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat
+.HP
+\fB\-mem\fR [int] : specify the amount of memory that cplex is allowed to use
+.HP
+\fB\-maxReportedHits\fR [int] : if using BWA as mapping tool, specify the maximal number of reported hits, DEFAULT: 2
+.HP
+\fB\-prokaryote\fR : if specified, genome is treated as prokaryotic, no spliced reads are accepted, and structural genes are resolved. DEFAULT: n
+.HP
+\fB\-minCov\fR [double] : specify the minimum required coverage of the gene candidate extraction, DEFAULT: \fB\-1\fR (is estimated from mapping)
+.HP
+\fB\-maxCov\fR [double] : optional maximal coverage threshold, can also be estimated from mapping (DEFAULT)
+.HP
+\fB\-endCov\fR [double] : if the coverage falls below this value, the currently open candidate gene is closed. This value can be estimated from the minimum coverage (\fB\-1\fR); DEFAULT: \fB\-1\fR
+.HP
+\fB\-dispCov\fR [0/1] : estimate (1) the coverage histogram for the read mapping, DEFAULT: 0
+.HP
+\fB\-interval\fR [int] : specify the minimal size of an interval between near candidate genes, if "\-1" it equals the read length. DEFAULT: \fB\-1\fR
+.HP
+\fB\-splLim\fR [double] : specify the minimal coverage that is required to accept a splice site, if (\fB\-1\fR) the threshold is equal to minCov, DEFAULT: \fB\-1\fR
+.HP
+\fB\-rL\fR [int] : specify read length, otherwise this information is extracted from SAM file (DEFAULT)
+.HP
+\fB\-samForSequential\fR [pathToSamFile] : if it is desired to analyse chromosomes in a sequential manner, provide a chromosome sorted sam file in addition to the one sorted by read names, DEFAULT: noSequential
+.HP
+\fB\-noAmbiOpti\fR : if specified, ambiguous hits are not included in the analysis
+.HP
+\fB\-settingMapper\fR [(list of parameters)] : A comma\-separated list of the desired parameters for TopHat or BWA. Please provide
+.IP
+for each parameter a pair of indicator and value, separated by an equality sign.
+Note that paramters intended for the 3 different parts (indexing, aln, sam) of BWA have to be separated by a lowercase bar
+.IP
+Example: \fB\-settingMapper\fR [\-a=is_\-t=5,\-N_\-n=5]
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
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