annotate strelka.xml @ 17:8260a4188b08

solved conf_file.ini pb
author mini
date Wed, 01 Oct 2014 13:45:33 +0200
parents 024468e8638c
children 3c10d88b55ad
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
bce06de6cea2 modified help section
mini
parents: 10
diff changeset
1 <tool id="strelka" name="Strelka" version="1.0.0">
10
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
2 <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
3 <description>Strelka</description>
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
4 <requirements>
14
ca84a74ff567 corriging bug in environment variable
mini
parents: 10
diff changeset
5 <requirement type="set_environment">SCRIPT_PATH_STRELKA</requirement>
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
6 <requirement type="package" version="0.1.18">samtools</requirement>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
7 <requirement type="package" version="0.1.11">vcftools</requirement>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
8 </requirements>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
9 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
10 #if $configuration.configuration_switch == 'Default':
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
11 --configFile Default
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
12 #else if $configuration.configuration_switch == 'Path':
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
13 --configFile $configuration.configFile
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
14 #else:
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
15 --configFile Custom
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
16 --depthFilterMultiple $configuration.depthFilterMultiple
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
17 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
18 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
19 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
20 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
21 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
22 --ssnvPrior $configuration.ssnvPrior
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
23 --sindelPrior $configuration.sindelPrior
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
24 --ssnvNoise $configuration.ssnvNoise
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
25 --sindelNoise $configuration.sindelNoise
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
26 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
27 --minTier1Mapq $configuration.minTier1Mapq
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
28 --minTier2Mapq $configuration.minTier2Mapq
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
29 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
30 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
31 --isWriteRealignedBam $configuration.isWriteRealignedBam
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
32 --binSize $configuration.binSize
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
33 --isSkipDepthFilters $configuration.isSkipDepthFilters
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
34 --maxInputDepth $configuration.maxInputDepth
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
35 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
36 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
37 #end if
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
38 #end if
16
024468e8638c environment variable
mini
parents: 15
diff changeset
39 --scriptPath \$SCRIPT_PATH_STRELKA
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
40 </command>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
41
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
42 <inputs>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
43 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
44 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
45 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
46
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
47 <conditional name="configuration">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
48 <param name="configuration_switch" type="select" label="how do you want to configure strelka">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
49 <option value="Default" selected="true">Default</option>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
50 <option value="Path">Use a config file</option>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
51 <option value="Custom">Custom</option>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
52 </param>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
53 <when value="Default">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
54 <!-- do nothing -->
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
55 </when>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
56 <when value="Path">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
57 <param format="ini" name="configFile" type="data" label="config file"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
58 </when>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
59 <when value="Custom">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
60 <param name="binSize" type="integer" value="25000000" label="binSize" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
61 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
62 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
10
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
63 <param name="isWriteRealignedBam" type="integer" value="0" min="0" max="1" label="isWriteRealignedBam" help="0 for no alignment else 1"/>
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
64 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
65 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
66 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
67 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
68 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
69 <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
70 <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
71 <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
72 <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
73 <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
74 <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
75 <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
76 <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
77 <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
78 <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
79 <conditional name="extra_arguments">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
80 <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
81 <option value="No" selected="true">No</option>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
82 <option value="Yes">Yes</option>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
83 </param>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
84 <when value="No">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
85 <!-- do nothing -->
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
86 </when>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
87 <when value="Yes">
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
88 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
89 </when>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
90 </conditional>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
91 </when>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
92 </conditional>
10
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
93 <param name="conf_file_check" type="boolean" label="output conf file" checked="False"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
94 <param name="output1_file_check" type="boolean" label="output passed snvs(filtred)" checked="True"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
95 <param name="output2_file_check" type="boolean" label="output passed indels(filtred)" checked="True"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
96 <param name="output3_file_check" type="boolean" label="output all snvs" checked="True"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
97 <param name="output4_file_check" type="boolean" label="output all indels" checked="True"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
98 <param name="output5_file_check" type="boolean" label="normal realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
99 <param name="output6_file_check" type="boolean" label="tumor realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
100
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
101 </inputs>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
102
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
103 <outputs>
10
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
104 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
105 <filter>output1_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
106 </data>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
107 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
108 <filter>output2_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
109 </data>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
110 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
111 <filter>output3_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
112 </data>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
113 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
114 <filter>output4_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
115 </data>
17
8260a4188b08 solved conf_file.ini pb
mini
parents: 16
diff changeset
116 <data format="tabular" name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/config.ini">
10
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
117 <filter>conf_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
118 </data>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
119 <data format="bam" name="output5_bam" label="${tool.name} on ${on_string}(normal.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/normal.realigned.bam">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
120 <filter>output5_file_check == True</filter>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
121 </data>
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
122 <data format="bam" name="output6_bam" label="${tool.name} on ${on_string}(tumor.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/tumor.realigned.bam">
f66f23fcc83a Modified layout
mini
parents: 7
diff changeset
123 <filter>output6_file_check == True</filter>
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
124 </data>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
125 </outputs>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
126
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
127 <tests>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
128 <test>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
129 <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
130 <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
131 <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
132 <param name="configuration_switch" value="Default"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
133 <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
134 <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
135 <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
136 <output name="output4_vcf" file="all.somatic.indels.vcf"/>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
137 </test>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
138 </tests>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
139
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
140 <help>
13
bce06de6cea2 modified help section
mini
parents: 10
diff changeset
141 Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples.
bce06de6cea2 modified help section
mini
parents: 10
diff changeset
142 You can see more information at : https://sites.google.com/site/strelkasomaticvariantcaller
6
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
143 </help>
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
144
87568e5a7d4f Testing strelka version 0.0.1
mini
parents:
diff changeset
145 </tool>