[med-svn] [seqsero] 02/03: Fix usage

[Andreas Tille]

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tille pushed a commit to branch master
in repository seqsero.

commit 8dfe4d6468679761bd44b7b9cc8c50d8be2e6359
Author: Andreas Tille <tille at debian.org>
Date:   Tue Apr 4 09:25:35 2017 +0200

    Fix usage
---
 debian/patches/fix_usage.patch | 16 ++++++++++++++++
 debian/patches/series          |  1 +
 2 files changed, 17 insertions(+)

diff --git a/debian/patches/fix_usage.patch b/debian/patches/fix_usage.patch
new file mode 100644
index 0000000..59b5722
--- /dev/null
+++ b/debian/patches/fix_usage.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 15 Feb 2017 09:17:30 +0100
+Description: In Debian you do not call the Python script but
+ rather a renamed wrapper.  Also fix spelling issue
+
+--- a/SeqSero.py
++++ b/SeqSero.py
+@@ -8,7 +8,7 @@
+ import argparse,os,sys,time,random
+ 
+ def main():
+-  parser = argparse.ArgumentParser(usage='SeqSero.py -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk at uga.edu) and Xiangyu Deng (xdeng at uga.edu)\n\nContact email:seqsero at gmail.com')
++  parser = argparse.ArgumentParser(usage='seqsero -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDeveloper: Shaokang Zhang (zskzsk at uga.edu) and Xiangyu Deng (xdeng at uga.edu)\n\nContact email:seqsero at gmail.com')
+   parser.add_argument("-m", choices=['1','2','3', '4'],help="<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)")
+   parser.add_argument("-i", nargs="+", help="<string>: path/to/input_data")
+   parser.add_argument("-b",choices=['sam','mem'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam") 
diff --git a/debian/patches/series b/debian/patches/series
index 471416f..1e63e3d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 fix_perl_interpreter.patch
+fix_usage.patch

-- 
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