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comparison macro_main.xml @ 22:1c8dcda28be7

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version 27/11/2014, corrected extra arguments bug
author mini
date Thu, 27 Nov 2014 10:31:58 +0100
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21:f785839fb395 22:1c8dcda28be7
1 <macros>
2 <macro name="main">
3 <description>Strelka</description>
4 <requirements>
5 <requirement type="set_environment">SCRIPT_PATH_STRELKA</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="0.1.11">vcftools</requirement>
8 </requirements>
9 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam
10 #silent sys.stderr.write("!!!! Cheetah Template Variables !!!!\n")
11 #for k,v in $searchList[2].items()
12 #silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
13 #end for
14 #silent sys.stderr.write("!!!! end-of-list !!!!\n")
15 #import string
16
17 --scriptPath \$SCRIPT_PATH_STRELKA
18 #if $genomeSource.refGenomeSource == "history":
19 --refFile "${genomeSource.ownFile}"
20 #else:
21 --refFile "${genomeSource.index.fields.path}"
22 #end if
23
24 #if $configuration.configuration_switch == 'Default for Bwa':
25 --configFile strelka_config_bwa_default.ini
26 #else if $configuration.configuration_switch == 'Default for Isaac':
27 --configFile strelka_config_isaac_default.ini
28 #else if $configuration.configuration_switch == 'Default for Eland':
29 --configFile strelka_config_eland_default.ini
30 #else if $configuration.configuration_switch == 'Path':
31 --configFile $configuration.configFile
32 #else:
33 --configFile Custom
34 --depthFilterMultiple $configuration.depthFilterMultiple
35 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
36 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
37 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
38 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
39 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
40 --ssnvPrior $configuration.ssnvPrior
41 --sindelPrior $configuration.sindelPrior
42 --ssnvNoise $configuration.ssnvNoise
43 --sindelNoise $configuration.sindelNoise
44 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
45 --minTier1Mapq $configuration.minTier1Mapq
46 --minTier2Mapq $configuration.minTier2Mapq
47 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
48 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
49 --isWriteRealignedBam $configuration.isWriteRealignedBam
50 --binSize $configuration.binSize
51 --isSkipDepthFilters $configuration.isSkipDepthFilters
52 --maxInputDepth $configuration.maxInputDepth
53 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
54 --extraStrelkaArguments yes
55 #if $configuration.extra_arguments.a:
56 -a
57 #end if
58 #if $configuration.extra_arguments.b:
59 -b $configuration.extra_arguments.barg
60 #end if
61 #if $configuration.extra_arguments.c:
62 -c $configuration.extra_arguments.carg
63 #end if
64 #if $configuration.extra_arguments.d:
65 -d $configuration.extra_arguments.darg
66 #end if
67 #if $configuration.extra_arguments.e:
68 -e $configuration.extra_arguments.earg
69 #end if
70 #end if
71 #end if
72
73 </command>
74 </macro>
75 </macros>
76