Mercurial > repos > rnateam > segemehl

comparison segemehl.xml @ 2:0da425524259 draft

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author bgruening
date Thu, 05 Feb 2015 08:25:13 -0500
parents df7c7d732d31
children 039547ad8fb8
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1:df7c7d732d31 2:0da425524259
8 ## prepare segemehl index if no reference genome is supplied 8 ## prepare segemehl index if no reference genome is supplied
9 temp_index = `mktemp`; 9 temp_index = `mktemp`;
10 #if $refGenomeSource.genomeSource == "history": 10 #if $refGenomeSource.genomeSource == "history":
11 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome; 11 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
12 #else: 12 #else:
13 #set $temp_index = ${refGenomeSource.index.fields.index_path} 13 #set $temp_index = $refGenomeSource.index.fields.index_path
14 #end if 14 #end if
15 15
16 16
17 ## execute segemehl 17 ## execute segemehl
18 segemehl.x 18 segemehl.x
50 #end if 50 #end if
51 -m $minsize 51 -m $minsize
52 -A $accuracy 52 -A $accuracy
53 -H $hitstrategy 53 -H $hitstrategy
54 #if str( $prime5 ).strip(): 54 #if str( $prime5 ).strip():
55 -P $prime5 55 -P "$prime5"
56 #end if 56 #end if
57 #if str( $prime3 ).strip(): 57 #if str( $prime3 ).strip():
58 -Q $prime3 58 -Q "$prime3"
59 #end if 59 #end if
60 $polyA 60 $polyA
61 $autoclip 61 $autoclip
62 $hardclip 62 $hardclip
63 $order 63 $order