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commit 38c33bebed42e8b8e16a5c64beeb777cbe14e7bb Author: Sascha Steinbiss <sas...@steinbiss.name> Date: Tue Jun 7 21:33:49 2016 +0000 add man page --- debian/control | 4 ++- debian/manpages | 1 + debian/rules | 7 +++++ debian/sspace.1.adoc | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 93 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index fc8bb7d..6932be1 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,9 @@ Uploaders: Andreas Tille <ti...@debian.org> Section: science Priority: optional Build-Depends: debhelper (>= 9), - recode + recode, + python, + asciidoctor Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sspace.git Vcs-Git: https://anonscm.debian.org/git/debian-med/sspace.git diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..f52cc9b --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/sspace.1 diff --git a/debian/rules b/debian/rules index 91b7b89..8c54dc0 100755 --- a/debian/rules +++ b/debian/rules @@ -5,7 +5,14 @@ %: dh $@ +override_dh_auto_clean: + dh_auto_clean + rm -f debian/sspace.1 + override_dh_install: dh_install find debian -name "*.pl" -exec recode ibmpc.. \{\} \; +override_dh_installman: + asciidoctor -a docdate='' -b manpage debian/sspace.1.adoc + dh_installman diff --git a/debian/sspace.1.adoc b/debian/sspace.1.adoc new file mode 100644 index 0000000..7d1de48 --- /dev/null +++ b/debian/sspace.1.adoc @@ -0,0 +1,82 @@ +# sspace(1) + +## NAME + +sspace - SSPACE-basic scaffolding tool + +## SYNOPSIS + +*sspace* [options] -l [libraryfilename] -s [contigfilename] + +## DESCRIPTION + +SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination. + +Please read the README file at /usr/share/doc/sspace/README.gz for more information. + +## OPTIONS + +### General Parameters + + *-l*:: + Library file containing two paired read files with insert size, error and either mate pair or paired end indication (REQUIRED) + + *-s*:: + FASTA file containing contig sequences used for extension. Inserted pairs are mapped to extended and non-extended contigs (REQUIRED) + + *-x*:: + Indicate whether to extend the contigs of -s using paired reads in -l (-x 1=extension, -x 0=no extension, default -x 0) + +### Extension Parameters + + *-m*:: + Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 32) + + *-o*:: + Minimum number of reads needed to call a base during an extension (default -o 20) + + *-t*:: + Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0) + + *-u*:: + FASTA/FASTQ file containing unpaired sequence reads (optional) + + *-r*:: + Minimum base ratio used to accept a overhang consensus base (default -r 0.9) + +### Scaffolding Parameters + + *-z*:: + Minimum contig length used for scaffolding. Filters out contigs below this value (default -z 0) + + *-k*:: + Minimum number of links (read pairs) to compute scaffold (default -k 5) + + *-a*:: + Maximum link ratio between two best contig pairs. *Higher values lead to least accurate scaffolding* (default -a 0.7) + + *-n*:: + Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n 15) + +### Bowtie Parameters + + *-g*:: + Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie. Higher number of allowed gaps can lead to least accurate scaffolding. (default -g 0) + + *-T*:: + Specify the number of threads in Bowtie. Corresponds to the -p/--threads option in Bowtie (default -T 1) + +### Additional Parameters + + *-b*:: + Base name for your output files (default -b standard_output) + + *-v*:: + Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0) + + *-p*:: + Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0) + +## AUTHORS + +Marten Boetzer, Walter Pirovano, Nicola Soranzo -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sspace.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit