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Updated Lastz tests with comments

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This commit is contained in:
Kelly Vincent
2009-12-02 15:23:15 -05:00
parent c53e0d626f
commit f446bce0c1
2 changed files with 19 additions and 18 deletions
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tools/sr_mapping/lastz_wrapper.py
+1 -1
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@@ -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 )
tools/sr_mapping/lastz_wrapper.xml
+18 -17
View File
@@ -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" />