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comparison shear_sv.xml @ 3:630532975fa9

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Fix more typos
author Jim Johnson <jj@umn.edu>
date Mon, 08 Jul 2013 01:10:38 -0500
parents 239e200ae99f
children a82400332451
comparison
equal deleted inserted replaced
2:239e200ae99f 3:630532975fa9
9 <requirement type="package" version="latest">kent</requirement> 9 <requirement type="package" version="latest">kent</requirement>
10 </requirements> 10 </requirements>
11 <!-- 11 <!--
12 <version_command></version_command> 12 <version_command></version_command>
13 --> 13 -->
14 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar sv -r $prefix 14 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar sv -p $prefix
15 -b $bamfile 15 -b $bamfile
16 #if $genomeSource.refGenomeSource == 'indexed': 16 #if $genomeSource.refGenomeSource == 'indexed':
17 -f $genomeSource.ref_fastas.fields.path 17 -f $genomeSource.ref_fastas.fields.path
18 -i $genomeSource.bwa_indices.fields.path 18 -i $genomeSource.bwa_indices.fields.path
19 -t $genomeSource.twobit_indices.fields.paths 19 -t $genomeSource.twobit_indices.fields.path
20 #else: 20 #else:
21 -f $genomeSource.ref_fasta 21 -f $genomeSource.ref_fasta
22 -i $genomeSource.bwa_index 22 -i $genomeSource.bwa_index
23 -t $genomeSource.twobit 23 -t $genomeSource.twobit
24 #end if 24 #end if