[med-svn] [Git][med-team/graphbin][master] Write manpage

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / graphbin


Commits:
8d66d9ae by Shayan Doust at 2020-07-16T17:21:08+01:00
Write manpage

- - - - -


2 changed files:

- + debian/graphbin.manpages
- + debian/mans/graphbin.1


Changes:

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debian/graphbin.manpages
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+debian/mans/*.1


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debian/mans/graphbin.1
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+.TH GRAPHBIN "1" "July 2020" "graphbin" "User Commands"
+.SH NAME
+graphbin \- refined binning of metagenomic contigs using assembly graphs
+.SH SYNOPSIS
+usage: graphbin [\fI\,-h\/\fR] \fB\-\-assembler\fR \fI\,ASSEMBLER\/\fR \fB\-\-graph\fR \fI\,GRAPH\/\fR [\-\-paths \fI\,PATHS\/\fR]
+\fB\-\-binned\fR \fI\,BINNED\/\fR \fB\-\-output\fR \fI\,OUTPUT\/\fR [\-\-prefix \fI\,PREFIX\/\fR]
+[\-\-max_iteration \fI\,MAX_ITERATION\/\fR]
+[\-\-diff_threshold\fI\, DIFF_THRESHOLD\/\fR]
+.SH DESCRIPTION
+.PP
+GraphBin is a metagenomic contig binning tool that makes use of
+the contig connectivity information from the assembly graph to bin contigs. It
+utilizes the binning result of an existing binning tool and a label
+propagation algorithm to correct mis\-binned contigs and predict the labels of
+contigs which are discarded due to short length.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-assembler\fR ASSEMBLER
+name of the assembler used (SPAdes, SGA or MEGAHIT).
+GraphBin supports Flye, Canu and Miniasm long\-read
+assemblies as well.
+.TP
+\fB\-\-graph\fR GRAPH
+path to the assembly graph file
+.TP
+\fB\-\-paths\fR PATHS
+path to the contigs.paths file
+.TP
+\fB\-\-binned\fR BINNED
+path to the .csv file with the initial binning output
+from an existing tool
+.TP
+\fB\-\-output\fR OUTPUT
+path to the output folder
+.TP
+\fB\-\-prefix\fR PREFIX
+prefix for the output file
+.TP
+\fB\-\-max_iteration\fR MAX_ITERATION
+maximum number of iterations for label propagation
+algorithm. [default: 100]
+.TP
+\fB\-\-diff_threshold\fR DIFF_THRESHOLD
+difference threshold for label propagation algorithm.
+[default: 0.1]



View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648

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View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648
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