[med-svn] [qcumber] 01/07: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 41a2cbad0bba5915f2a0caf25daddd0d7d22c27b
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 30 08:28:16 2016 +0100

    Add manpage
---
 debian/control   |   2 +-
 debian/manpages  |   1 +
 debian/qcumber.1 | 105 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 107 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index db1cbeb..6c96917 100644
--- a/debian/control
+++ b/debian/control
@@ -35,7 +35,7 @@ Conflicts: qc-pipeline
 Provides: qc-pipeline
 Replaces: qc-pipeline
 Description: quality control of genomic sequences
- QCPipeline is a tool for quality control. The workflow is as followed:
+ QCPipeline is a tool for quality control. The workflow is as follows:
  .
   1. Quality control with FastQC
   2. Trim Reads with Trimmomatic
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
diff --git a/debian/qcumber.1 b/debian/qcumber.1
new file mode 100644
index 0000000..33d5156
--- /dev/null
+++ b/debian/qcumber.1
@@ -0,0 +1,105 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH QCUMBER "1" "November 2016" "qcumber 1.0.1" "User Commands"
+.SH NAME
+qcumber \- quality control of genomic sequences
+.SH SYNOPSIS
+.Bqcumber
+ [\-h] [\-input INPUT] [\-1 R1] [\-2 R2] [\-output OUTPUT]
+\fB\-technology\fR {Illumina,IonTorrent} [\-threads THREADS]
+[\-adapter {TruSeq2\-PE,TruSeq2\-SE,TruSeq3\-PE,TruSeq3\-SE,TruSeq3\-PE\-2,NexteraPE\-PE}]
+[\-reference REFERENCE] [\-index INDEX] [\-sav SAV]
+[\-save_mapping] [\-db DB] [\-palindrome PALINDROME]
+[\-minlen MINLEN] [\-trimOption TRIMOPTION] [\-version]
+[\-nokraken] [\-nomapping] [\-trimBetter]
+[\-trimBetter_threshold TRIMBETTER_THRESHOLD] [\-forAssembly]
+[\-forMapping]
+.SH DESCRIPTION
+QCPipeline is a tool for quality control. The workflow is as follows:
+.nr step 1 1
+.IP \n[step] 3
+Quality control with FastQC
+.IP \n+[step]
+Trim Reads with Trimmomatic
+.IP \n+[step]
+Quality control of trimmed reads with FastQC
+.IP \n+[step]
+Map reads against reference using bowtie2
+.IP \n+[step]
+Classify reads with Kraken
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-input\fR INPUT
+input sample folder. Illumina filenames have to end
+with _<lane>_<R1|R2>_number, e.g.
+Sample_12_345_R1_001.fastq
+.TP
+\fB\-1\fR R1
+input file. Illumina filename must not match
+<project>_<lane>_<R1|R2>_<number> name pattern
+.TP
+\fB\-2\fR R2
+input file
+.HP
+\fB\-output\fR OUTPUT
+.HP
+\fB\-technology\fR {Illumina,IonTorrent}
+.HP
+\fB\-threads\fR THREADS
+.HP
+\fB\-adapter\fR {TruSeq2\-PE,TruSeq2\-SE,TruSeq3\-PE,TruSeq3\-SE,TruSeq3\-PE\-2,NexteraPE\-PE}
+.TP
+\fB\-reference\fR REFERENCE
+Map reads against reference
+.TP
+\fB\-index\fR INDEX
+Bowtie2 index if available.
+.TP
+\fB\-sav\fR SAV
+Illumina folder for SAV. Requires RunInfo.xml,
+RunParamter.xml and Interop folder.
+.HP
+\fB\-save_mapping\fR
+.TP
+\fB\-db\fR DB
+Kraken database
+.TP
+\fB\-palindrome\fR PALINDROME
+Use palindrome parameter 30 or 1000 for further
+analysis. Default:30
+.TP
+\fB\-minlen\fR MINLEN
+Minlen parameter for Trimmomatic. Default:50
+.TP
+\fB\-trimOption\fR TRIMOPTION
+Use maxinfo or slidinginfo for
+Trimmomatic.MAXINFO:<target length>:<strictness> |
+SLIDINGWINDOW:<window size>:<required quality>.
+default: SLIDINGWINDOW:4:15
+.TP
+\fB\-version\fR
+show program's version number and exit
+.HP
+\fB\-nokraken\fR
+.HP
+\fB\-nomapping\fR
+.TP
+\fB\-trimBetter\fR
+Optimize trimming parameter using 'Per sequence base
+content' from fastqc. Not recommended for amplicons.
+.TP
+\fB\-trimBetter_threshold\fR TRIMBETTER_THRESHOLD
+Set \fB\-trimBetter\fR to use this option.Default setting for
+Illumina: 0.15 and for IonTorrent: 0.25.
+.TP
+\fB\-forAssembly\fR
+Set \fB\-trimBetter\fR to use this option.Trim parameter are
+optimized for assemblies (trim more aggressive).
+.TP
+\fB\-forMapping\fR
+Set \fB\-trimBetter\fR to use this option.Trim parameter are
+optimized for mapping (allow more errors).
+.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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