Mercurial > repos > mini > strelka
comparison strelka.xml @ 10:f66f23fcc83a
Modified layout
author | mini |
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date | Tue, 30 Sep 2014 11:08:39 +0200 |
parents | 3e8541ece3c7 |
children | bce06de6cea2 ca84a74ff567 |
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8:2cee4ed50058 | 10:f66f23fcc83a |
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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> |