[med-svn] [gasic] 01/01: Add manpages by editing help2man output
Andreas Tille
tille at debian.org
Wed Feb 12 10:13:27 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gasic.
commit 0f35290cdd410d01e1e85bc52e353c70c853198e
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 12 11:04:24 2014 +0100
Add manpages by editing help2man output
---
debian/control | 2 +-
debian/createmanpages | 15 ++++++++++++
debian/manpages | 1 +
debian/mans/correct_abundances.1 | 39 ++++++++++++++++++++++++++++++++
debian/mans/create_matrix.1 | 49 ++++++++++++++++++++++++++++++++++++++++
debian/mans/quality_check.1 | 23 +++++++++++++++++++
debian/mans/run_mappers.1 | 38 +++++++++++++++++++++++++++++++
7 files changed, 166 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 2ca7ba9..45a48c3 100644
--- a/debian/control
+++ b/debian/control
@@ -21,7 +21,7 @@ Depends: ${misc:Depends},
bowtie2,
bwa,
seqan-apps
-Description: Genome Abundance Similarity Correction
+Description: genome abundance similarity correction
One goal of sequencing based metagenomic analysis is the quantitative
taxonomic assessment of microbial community compositions. However, the
majority of approaches either quantify at low resolution (e.g. at phylum
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..f7c362e
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,15 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+help2man --no-info --no-discard-stderr \
+ --name='run the genome abundance similarity correction step' \
+ --version-string='SVNr18' correct_abundances > $MANDIR/correct_abundances.1
+help2man --no-info --no-discard-stderr \
+ --name='calculate the genome abundance similarity matrix' \
+ --version-string='SVNr18' create_matrix > $MANDIR/create_matrix.1
+help2man --no-info --no-discard-stderr \
+ --name='perform a sanity check on the mapping results (SAM file)' \
+ --version-string="SVNr18" quality_check > $MANDIR/quality_check.1
+help2man --no-info --no-discard-stderr \
+ --name='run a read mapper to map reads to reference genomes' \
+ --version-string="SVNr18" run_mappers > $MANDIR/run_mappers.1
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/correct_abundances.1 b/debian/mans/correct_abundances.1
new file mode 100644
index 0000000..14a87b9
--- /dev/null
+++ b/debian/mans/correct_abundances.1
@@ -0,0 +1,39 @@
+.TH CORRECT_ABUNDANCES "1" "February 2014" "correct_abundances SVNr18" "User Commands"
+.SH NAME
+correct_abundances \- run the genome abundance similarity correction step
+.SH SYNOPSIS
+.B correct_abundances
+\fINAMES\fR
+.SH DESCRIPTION
+Run the similarity correction step.
+.PP
+Note: Although it is possible to run the read mappers by hand or to create the
+similarity matrix manually, we strongly recommend to use the provided Python
+scripts 'run_mappers.py' and 'create_similarity_matrix.py'.
+.SH OPTIONS
+.TP
+\fINAMES\fR:
+Filename of the names file; the plain text names file should
+contain one name per line. The name is used as identifier in
+the whole algorithm.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-m\fR SMAT, \fB\-\-similarity\-matrix\fR=\fISMAT\fR
+Path to similarity matrix file. The similarity matrix
+must be created with the same NAMES file. [default:
+\&./similarity_matrix.npy]
+.TP
+\fB\-s\fR SAM, \fB\-\-samfiles\fR=\fISAM\fR
+Pattern pointing to the SAM files created by the
+mapper. Placeholder for the name is "%s". [default:
+\&./SAM/%s.sam]
+.TP
+\fB\-b\fR BOOT, \fB\-\-bootstrap\-samples\fR=\fIBOOT\fR
+Set the number of bootstrap samples. Use 1 to disable
+bootstrapping [default: 100]
+.TP
+\fB\-o\fR OUT, \fB\-\-output\fR=\fIOUT\fR
+Plain text output file containing the results.
+[default: ./results.txt]
diff --git a/debian/mans/create_matrix.1 b/debian/mans/create_matrix.1
new file mode 100644
index 0000000..94e292f
--- /dev/null
+++ b/debian/mans/create_matrix.1
@@ -0,0 +1,49 @@
+.TH CREATE_MATRIX "1" "February 2014" "create_matrix SVNr18" "User Commands"
+.SH NAME
+create_matrix \- calculate the genome abundance similarity matrix
+.SH SYNOPSIS
+.B create_matrix
+[\fIoptions\fR] \fINAMES\fR
+.SH DESCRIPTION
+Calculate the similarity matrix.
+.PP
+First, a set of reads is simulated for every reference genome using a read
+simulator from core/tools.py specified via \fB\-s\fR.
+Second, the simulated reads of each species are mapped against all reference
+genomes using the mapper specified with \fB\-m\fR.
+Third, the resulting SAM\-files are analyzed to calculate the similarity
+matrix. The similarity matrix is stored as a numpy file (\fB\-o\fR).
+.SH OPTIONS
+.TP
+\fBNAMES\fR
+Filename of the names file; the plain text names file should
+contain one name per line. The name is used as identifier in
+the whole algorithm.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-s\fR SIMULATOR, \fB\-\-simulator\fR=\fISIMULATOR\fR
+Identifier of read simulator defined in core/tools.py
+[default: none]
+.TP
+\fB\-r\fR REF, \fB\-\-reference\fR=\fIREF\fR
+Reference sequence file pattern for the read
+simulator. Placeholder for the name is "%s". [default:
+\&./ref/%s.fasta]
+.TP
+\fB\-m\fR MAPPER, \fB\-\-mapper\fR=\fIMAPPER\fR
+Identifier of mapper defined in core/tools.py
+[default: none]
+.TP
+\fB\-i\fR INDEX, \fB\-\-index\fR=\fIINDEX\fR
+Reference index files for the read mapper. Placeholder
+for the name is "%s". [default: ./ref/%s.fasta]
+.TP
+\fB\-t\fR TEMP, \fB\-\-temp\fR=\fITEMP\fR
+Directory to store temporary simulated datasets and
+SAM files. [default: ./temp]
+.TP
+\fB\-o\fR OUT, \fB\-\-output\fR=\fIOUT\fR
+Output similarity matrix file. [default:
+\&./similarity_matrix.npy]
diff --git a/debian/mans/quality_check.1 b/debian/mans/quality_check.1
new file mode 100644
index 0000000..7aadc96
--- /dev/null
+++ b/debian/mans/quality_check.1
@@ -0,0 +1,23 @@
+.TH QUALITY_CHECK "1" "February 2014" "quality_check SVNr18" "User Commands"
+.SH NAME
+quality_check \- perform a sanity check on the mapping results (SAM file)
+.SH SYNOPSIS
+.B quality_check
+[\fIOptions\fR] \fISAMFILE\fR
+.SH DESCRIPTION
+Perform a sanity check on the mapping results (SAM file).
+.PP
+This tool analyzes the output of the read mapper and provides useful
+information to the user to decide whether the set of reference sequences
+and the mapper settings are feasible for the given dataset.
+.SH OPTIONS
+.TP
+\fBSAMFILE\fR
+Name of the SAM file to analyze
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-o\fR OUT, \fB\-\-outpath\fR=\fIOUT\fR
+Path to the directory for the analysis output.
+[default: ./]
diff --git a/debian/mans/run_mappers.1 b/debian/mans/run_mappers.1
new file mode 100644
index 0000000..e4b58eb
--- /dev/null
+++ b/debian/mans/run_mappers.1
@@ -0,0 +1,38 @@
+.TH RUN_MAPPERS "1" "February 2014" "run_mappers SVNr18" "User Commands"
+.SH NAME
+run_mappers \- run a read mapper to map reads to reference genomes
+.SH SYNOPSIS
+.B run_mappers
+\fINAMES READS -i REF -o OUT -m MAPPER\fR
+.SH DESCRIPTION
+Run a read mapper to map reads to reference genomes.
+.PP
+The names in the NAMES file will be inserted in the provided string
+patterns. Each pattern must contain exactly one "%s" placeholder
+(python string formatting).
+.SH OPTIONS
+.TP
+\fINAMES\fR
+Filename of the names file; the plain text names file should
+contain one name per line. The name is used as identifier in
+the whole algorithm.
+.TP
+\fIREADS\fR
+File containing the reads to be mapped.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-m\fR MAPPER, \fB\-\-mapper\fR=\fIMAPPER\fR
+Identifier of mapper defined in core/tools.py
+[default: none]
+.TP
+\fB\-i\fR REF, \fB\-\-index\fR=\fIREF\fR
+Pattern, that points to the reference
+sequences/indices when used with a name. Placeholder
+for the name is "%s". [default: ./ref/%s.fasta]
+.TP
+\fB\-o\fR OUT, \fB\-\-output\fR=\fIOUT\fR
+Pattern, that points to the output SAM file, when used
+with a name. Placeholder for the name is "%s".
+[default: ./SAM/%s.sam]
--
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