[med-svn] [pipasic] 01/01: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository pipasic.

commit 7ae65dfe5c040051a8dc6cba6de6a98cce6cd1cd
Author: Andreas Tille <tille at debian.org>
Date:   Tue Sep 29 15:53:32 2015 +0200

    Add manpage
---
 debian/manpages  |  1 +
 debian/pipasic.1 | 93 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+)

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/pipasic.1 b/debian/pipasic.1
new file mode 100644
index 0000000..d6465e8
--- /dev/null
+++ b/debian/pipasic.1
@@ -0,0 +1,93 @@
+.TH PIPASIC "1" "September 2015" "pipasic 0.0+15" "User Commands"
+.SH NAME
+pipasic \- Protein Abundance Correction in Metaproteomic Data
+.SH SYNOPSIS
+.B pipasic.py
+\fI\,SPECTRA DB \/\fR[\fI\,module options\/\fR] [\fI\,input and configuration options\/\fR]
+.SH DESCRIPTION
+.PP
+Overall pipasic calling tool, including:
+.IP
+\- weighted (always) and unweighted (optional) similarity estimation
+(both sequence based)
+.IP
+\- correction, using matrix from similarity estimation
+.IP
+\- peptide Identification by InsPecT or Tide
+.TP
+SPECTRA: Comma\-separated string of spectrum files (mgf) \- without file\-extension!
+.TP
+DB:      Comma\-separated string of reference proteomes (fasta\-files) \- without file\-extension!
+if \fB\-S\fR or \fB\-I\fR: decoy database must exist as db_name+"_decoy.fasta"
+.PP
+Note: Pipasic requires two .fasta for each reference proteome <ref>:
+.IP
+\- "<ref>.fasta" containing the protein sequences only.
+.IP
+\- "<ref>_decoy.fasta" containing BOTH the protein AND decoy sequences. Decoy
+sequences must be tagged in their name with "REVERSED" or "DECOY" or any
+other tag specified by "\-t".
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-U\fR, \fB\-\-Unweighted\fR
+calculate unweighted similarities for all given
+proteomes
+.TP
+\fB\-I\fR, \fB\-\-Identify\fR
+identify given spectra with all given proteomes
+.TP
+\fB\-T\fR, \fB\-\-Tide\fR
+use Tide instead of InsPecT
+.TP
+\fB\-V\fR
+Visualize results using matplotlib
+.TP
+\fB\-o\fR OUTFILE, \fB\-\-outfile\fR=\fI\,OUTFILE\/\fR
+Output filename for results. Also serves as trunk for
+other result files (graphics, data).  [default:
+results.txt]
+.TP
+\fB\-s\fR SPEC_DIR, \fB\-\-spec_dir\fR=\fI\,SPEC_DIR\/\fR
+Directory of SPECTRA (mgf) files. Search in current
+directory, if not given. [default: none]
+.TP
+\fB\-d\fR DB_DIR, \fB\-\-db_dir\fR=\fI\,DB_DIR\/\fR
+Directory of proteinDBs. Search for DB files current
+directory, if not given. [default: none]
+.TP
+\fB\-m\fR MODS, \fB\-\-mods\fR=\fI\,MODS\/\fR
+A string containing all modifications in question,
+modification choice by filename if not given.
+[default: none]
+.TP
+\fB\-i\fR INSP_DIR, \fB\-\-inspect_dir\fR=\fI\,INSP_DIR\/\fR
+Inspect directory. [default: none]
+.TP
+\fB\-f\fR FDR, \fB\-\-fdr_cutoff\fR=\fI\,FDR\/\fR
+False discovery rate cut\-off for identification lists.
+[default: 0.05]
+.TP
+\fB\-t\fR DECOY_TAG, \fB\-\-decoy_tag\fR=\fI\,DECOY_TAG\/\fR
+Tag to identify decoy sequences in the database.
+Regular expressions may be used. This tag must be used
+in the name of all decoy sequences in the file
+"<DB>_decoy.fasta". [default: REVERSED|DECOY]
+.TP
+\fB\-l\fR LABELS, \fB\-\-labels\fR=\fI\,LABELS\/\fR
+Comma\-separated string of short names for organisms in
+the reference proteomes. If not given, the file name
+is used. [default: none]
+.TP
+\fB\-N\fR N, \fB\-\-N_spectra\fR=\fI\,N\/\fR
+Number of spectra in original dataset, comma\-separated
+list if multiple datasets. [default: none]
+.TP
+\fB\-c\fR COUNTS, \fB\-\-C_spectra\fR=\fI\,COUNTS\/\fR
+File containing numbers of spectra found by
+identification (Numpy Array dump). [default: none]
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+don't print status messages to stdout

-- 
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