From f446bce0c18ec0d0bb4f2c35ef6a60d8dcf57fe2 Mon Sep 17 00:00:00 2001
From: Kelly Vincent <kpvincent@bx.psu.edu>
Date: Wed, 2 Dec 2009 15:23:15 -0500
Subject: [PATCH] Updated Lastz tests with comments

---
 tools/sr_mapping/lastz_wrapper.py  |  2 +-
 tools/sr_mapping/lastz_wrapper.xml | 35 +++++++++++++++---------------
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/tools/sr_mapping/lastz_wrapper.py b/tools/sr_mapping/lastz_wrapper.py
index 7ddc9924f8b..b96559c7cca 100644
--- a/tools/sr_mapping/lastz_wrapper.py
+++ b/tools/sr_mapping/lastz_wrapper.py
@@ -121,7 +121,7 @@ def __main__():
         set_options = '--%s' % options.pre_set_options
     # Prepare for user-specified options
     else:
-        set_options = '--%s --%s --gapped --%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \
+        set_options = '--%s --%s --gapped --strand=%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \
                     ( options.gfextend, options.chain, options.strand, options.seed, 
                       options.transition, options.O, options.E, options.X, 
                       options.Y, options.K, options.L, options.entropy )
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 8baea0b698c..2335bb458b5 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -125,21 +125,10 @@
         <requirement type="binary">lastz</requirement>
     </requirements>
     <tests>
-        <test>
-            <param name="input2" value="b1.fasta" ftype="fasta" />
-            <param name="ref_source" value="history" />
-            <param name="input1" value="phiX.fasta" ftype="fasta" />
-            <param name="out_format" value="sam" />
-            <param name="source_select" value="pre_set" />
-            <param name="pre_set_options" value="yasra95short" />
-            <param name="how_to_name" value="no" />
-            <param name="min_ident" value="0" />
-            <param name="max_ident" value="100" />
-            <param name="min_cvrg" value="0" />
-            <param name="num_threads" value="4" />
-            <output name="output1" file="lastz_wrapper_out1.sam" />
-        </test>
-        <test>
+        <test> <!-- Lastz command: lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam 
+        			You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data 
+        			You will have to replace all the pluses 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="cached" />
             <param name="input1_2bit" value="phiX" />
@@ -157,6 +146,8 @@
             <param name="K" value="3000" />
             <param name="L" value="3000" />
             <param name="entropy" value="noentropy" />
+            <!-- how_to_name is not the default. It is changed to modify 
+            	 input1_2bit by adding the ref_name as a nickname -->
             <param name="how_to_name" value="yes" />
             <param name="ref_name" value="Ref" />
             <param name="min_ident" value="0" />
@@ -165,7 +156,10 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out2.sam" />
         </test>
-        <test>
+        <test> <!-- Lastz command: lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular 
+        			phiX.fasta and b1.fasta are located in galaxy's test-data 
+        			You will have to replace all the pluses 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.fasta" ftype="fasta" />
@@ -179,7 +173,14 @@
             <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"  />