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comparison strelka.xml @ 10:f66f23fcc83a

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Modified layout
author mini
date Tue, 30 Sep 2014 11:08:39 +0200
parents 3e8541ece3c7
children bce06de6cea2 ca84a74ff567
comparison
equal deleted inserted replaced
8:2cee4ed50058 10:f66f23fcc83a
1 <tool id="strelka88" name="Strelka good interface but no dependencies"> 1 <tool id="strelka" name="Strelka">
2 2 <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
3 <description>Strelka good interface but no dependencies</description> 3 <description>Strelka</description>
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">SCRIPT_PATH</requirement> 5 <requirement type="set_environment">SCRIPT_PATH</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement> 6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="0.1.11">vcftools</requirement> 7 <requirement type="package" version="0.1.11">vcftools</requirement>
8 </requirements> 8 </requirements>
58 </when> 58 </when>
59 <when value="Custom"> 59 <when value="Custom">
60 <param name="binSize" type="integer" value="25000000" label="binSize" /> 60 <param name="binSize" type="integer" value="25000000" label="binSize" />
61 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" /> 61 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
62 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" /> 62 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
63 <param name="isWriteRealignedBam" type="integer" value="0" label="isWriteRealignedBam" /> 63 <param name="isWriteRealignedBam" type="integer" value="0" min="0" max="1" label="isWriteRealignedBam" help="0 for no alignment else 1"/>
64 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" /> 64 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
65 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" /> 65 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
66 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" /> 66 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
67 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" /> 67 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
68 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" /> 68 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
88 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" /> 88 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
89 </when> 89 </when>
90 </conditional> 90 </conditional>
91 </when> 91 </when>
92 </conditional> 92 </conditional>
93 <conditional name="conf_file"> 93 <param name="conf_file_check" type="boolean" label="output conf file" checked="False"/>
94 <param name="conf_file_switch" type="select" label="output conf_file ?"> 94 <param name="output1_file_check" type="boolean" label="output passed snvs(filtred)" checked="True"/>
95 <option value="No" selected="true">No</option> 95 <param name="output2_file_check" type="boolean" label="output passed indels(filtred)" checked="True"/>
96 <option value="Yes">Yes</option> 96 <param name="output3_file_check" type="boolean" label="output all snvs" checked="True"/>
97 </param> 97 <param name="output4_file_check" type="boolean" label="output all indels" checked="True"/>
98 </conditional> 98 <param name="output5_file_check" type="boolean" label="normal realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
99 99 <param name="output6_file_check" type="boolean" label="tumor realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
100
101
102 100
103 </inputs> 101 </inputs>
104 102
105 <outputs> 103 <outputs>
106 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf"/> 104 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf">
107 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf"/> 105 <filter>output1_file_check == True</filter>
108 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"/> 106 </data>
109 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"/> 107 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf">
108 <filter>output2_file_check == True</filter>
109 </data>
110 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf">
111 <filter>output3_file_check == True</filter>
112 </data>
113 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf">
114 <filter>output4_file_check == True</filter>
115 </data>
110 <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini"> 116 <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
111 <filter>conf_file.conf_file_switch == "Yes"</filter> 117 <filter>conf_file_check == True</filter>
118 </data>
119 <data format="bam" name="output5_bam" label="${tool.name} on ${on_string}(normal.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/normal.realigned.bam">
120 <filter>output5_file_check == True</filter>
121 </data>
122 <data format="bam" name="output6_bam" label="${tool.name} on ${on_string}(tumor.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/tumor.realigned.bam">
123 <filter>output6_file_check == True</filter>
112 </data> 124 </data>
113 </outputs> 125 </outputs>
114 126
115 <tests> 127 <tests>
116 <test> 128 <test>