From f77f919f1268af7b8d77f54bf5cd59e8dd5c9c63 Mon Sep 17 00:00:00 2001
From: Kelly Vincent <kpvincent@bx.psu.edu>
Date: Mon, 7 Dec 2009 15:57:06 -0500
Subject: [PATCH] Changed Lastz call for tabular (general) format to suppress
 header

---
 tools/sr_mapping/lastz_wrapper.py  |  4 ++--
 tools/sr_mapping/lastz_wrapper.xml | 14 ++++++++++++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/tools/sr_mapping/lastz_wrapper.py b/tools/sr_mapping/lastz_wrapper.py
index b96559c7cca..7e3c5970076 100644
--- a/tools/sr_mapping/lastz_wrapper.py
+++ b/tools/sr_mapping/lastz_wrapper.py
@@ -2,7 +2,7 @@
 
 """
 Runs Lastz
-Written for Lastz v. 1.01.86.
+Written for Lastz v. 1.01.88.
 
 usage: lastz_wrapper.py [options]
     --ref_name: The reference name to change all output matches to
@@ -132,7 +132,7 @@ def __main__():
         input2 = options.input2
     if options.format == 'tabular':
         # Change output format to general if it's tabular and add field names for tabular output
-        format = 'general'
+        format = 'general-'
         tabular_fields = ':score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle'
     elif options.format == 'sam':
         # We currently ALWAYS suppress SAM headers.
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 4222b899aa8..5d3f2f30e6a 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="lastz_wrapper_2" name="Lastz" version="1.0.0">
+<tool id="lastz_wrapper_2" name="Lastz" version="1.1.0">
     <description> map short reads against reference sequence</description>
     <command interpreter="python">lastz_wrapper.py
 #if $seq_name.how_to_name=="yes":
@@ -179,7 +179,17 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out3.tabular" />
         </test>
-        <test>
+        <test> 
+        	<!-- 
+        	Lastz command: first you will need to split the file phiX_split.fasta into two files, 
+        	phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
+        	lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular 
+        	lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular 
+        	You need to point to phiX1.fasta and phiX2.fasta somewhere on your system. 
+        	phiX_split.fasta and b1.fasta are located in galaxy's test-data 
+        	You will have to replace all the asterisks before the commands with 2 dashes, 
+        	as double-dash can't appear in an XML comment 
+        	-->
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="history" />
             <param name="input1" value="phiX_split.fasta" ftype="fasta"  />