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comparison strelka2/strelka2.xml @ 0:7a9f20ca4ad5

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author mini
date Thu, 25 Sep 2014 11:59:08 -0400
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1 <tool id="strelka88" name="Strelka good interface but no dependencies">
2
3 <description>Strelka good interface but no dependencies</description>
4 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
5 #if $configuration.configuration_switch == 'Default':
6 --configFile Default
7 #else if $configuration.configuration_switch == 'Path':
8 --configFile $configuration.configFile
9 #else:
10 --configFile Custom
11 --depthFilterMultiple $configuration.depthFilterMultiple
12 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
13 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
14 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
15 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
16 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
17 --ssnvPrior $configuration.ssnvPrior
18 --sindelPrior $configuration.sindelPrior
19 --ssnvNoise $configuration.ssnvNoise
20 --sindelNoise $configuration.sindelNoise
21 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
22 --minTier1Mapq $configuration.minTier1Mapq
23 --minTier2Mapq $configuration.minTier2Mapq
24 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
25 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
26 --isWriteRealignedBam $configuration.isWriteRealignedBam
27 --binSize $configuration.binSize
28 --isSkipDepthFilters $configuration.isSkipDepthFilters
29 --maxInputDepth $configuration.maxInputDepth
30 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
31 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments
32 #end if
33 #end if
34 </command>
35
36 <inputs>
37 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
38 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
39 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
40
41 <conditional name="configuration">
42 <param name="configuration_switch" type="select" label="how do you want to configure strelka">
43 <option value="Default" selected="true">Default</option>
44 <option value="Path">Use a config file</option>
45 <option value="Custom">Custom</option>
46 </param>
47 <when value="Default">
48 <!-- do nothing -->
49 </when>
50 <when value="Path">
51 <param format="ini" name="configFile" type="data" label="config file"/>
52 </when>
53 <when value="Custom">
54 <param name="binSize" type="integer" value="25000000" label="binSize" />
55 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
56 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
57 <param name="isWriteRealignedBam" type="integer" value="0" label="isWriteRealignedBam" />
58 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
59 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
60 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
61 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
62 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
63 <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
64 <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
65 <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
66 <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
67 <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
68 <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
69 <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
70 <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
71 <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
72 <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
73 <conditional name="extra_arguments">
74 <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
75 <option value="No" selected="true">No</option>
76 <option value="Yes">Yes</option>
77 </param>
78 <when value="No">
79 <!-- do nothing -->
80 </when>
81 <when value="Yes">
82 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
83 </when>
84 </conditional>
85 </when>
86 </conditional>
87 <conditional name="conf_file">
88 <param name="conf_file_switch" type="select" label="output conf_file ?">
89 <option value="No" selected="true">No</option>
90 <option value="Yes">Yes</option>
91 </param>
92 </conditional>
93
94
95
96
97 </inputs>
98
99 <outputs>
100 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf"/>
101 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf"/>
102 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"/>
103 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"/>
104 <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
105 <filter>conf_file.conf_file_switch == "Yes"</filter>
106 </data>
107 </outputs>
108
109 <tests>
110 <test>
111 <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
112 <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
113 <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
114 <param name="configuration_switch" value="Default"/>
115 <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
116 <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
117 <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
118 <output name="output4_vcf" file="all.somatic.indels.vcf"/>
119 </test>
120 </tests>
121
122 <help>
123 Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
124 </help>
125
126 </tool>