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comparison FilterMutectCalls.xml @ 2:646e6943bcd2 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
author artbio
date Sun, 15 Oct 2023 12:06:24 +0000
parents c51c08cc9fcc
children
comparison
equal deleted inserted replaced
1:b040adcfeefd 2:646e6943bcd2
1 <tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="18.05"> 1 <tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="21.01">
2 <description>Filter variants in a GATK4 Mutect2 VCF callset</description> 2 <description>Filter variants in a GATK4 Mutect2 VCF callset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
89 <data format="tabular" name="output_vcf_bgzip_stats" label="${tool.name}: Filtered vcf (bgzip) statistics" from_work_dir="filtered.vcf.gz.filteringStats.tsv" > 89 <data format="tabular" name="output_vcf_bgzip_stats" label="${tool.name}: Filtered vcf (bgzip) statistics" from_work_dir="filtered.vcf.gz.filteringStats.tsv" >
90 <filter>input_options['input_options_selector'] == 'vcf_bgzip'</filter> 90 <filter>input_options['input_options_selector'] == 'vcf_bgzip'</filter>
91 </data> 91 </data>
92 </outputs> 92 </outputs>
93 <tests> 93 <tests>
94 <test> 94 <test expect_num_outputs="2">
95 <param name="reference_source_selector" value="history" /> 95 <param name="reference_source_selector" value="history" />
96 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 96 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
97 <conditional name="input_options"> 97 <conditional name="input_options">
98 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out1.vcf" /> 98 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out1.vcf" />
99 </conditional> 99 </conditional>
100 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out1.vcf.stats" /> 100 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out1.vcf.stats" />
101 <output name="output_vcf" file="filtered_Mutect2-out1.vcf" lines_diff="2" /> 101 <output name="output_vcf" file="filtered_Mutect2-out1.vcf" lines_diff="2" />
102 <output name="output_vcf_stats" file="filtered_Mutect2-out1_stats.tsv" /> 102 <output name="output_vcf_stats" file="filtered_Mutect2-out1_stats.tsv" />
103 </test> 103 </test>
104 <test> 104 <test expect_num_outputs="2">
105 <param name="reference_source_selector" value="history" /> 105 <param name="reference_source_selector" value="history" />
106 <param name="reference_sequence" ftype="fasta" value="chr20.fa" /> 106 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
107 <conditional name="input_options"> 107 <conditional name="input_options">
108 <param name="input_options_selector" value="vcf_bgzip" /> 108 <param name="input_options_selector" value="vcf_bgzip" />
109 <param name="unfiltered_vcf_input" ftype="vcf_bgzip" value="Mutect2-out6.vcf_bgzip" /> 109 <param name="unfiltered_vcf_input" ftype="vcf_bgzip" value="Mutect2-out6.vcf_bgzip" />
110 </conditional> 110 </conditional>
111 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out6.vcf_bgzip.stats" /> 111 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out6.vcf_bgzip.stats" />
112 <output name="output_vcf" file="filtered_Mutect2-out6.vcf_bgzip" compare="sim_size" /> 112 <output name="output_vcf" file="filtered_Mutect2-out6.vcf_bgzip" compare="sim_size" />
113 <output name="output_vcf_stats" file="filtered_Mutect2-out6_stats.tsv" /> 113 <output name="output_vcf_stats" file="filtered_Mutect2-out6_stats.tsv" />
114 </test> 114 </test>
115 <test> 115 <test expect_num_outputs="2">
116 <param name="reference_source_selector" value="history" /> 116 <param name="reference_source_selector" value="history" />
117 <param name="reference_sequence" ftype="fasta" value="chr20.fa" /> 117 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
118 <conditional name="input_options"> 118 <conditional name="input_options">
119 <param name="input_options_selector" value="vcf" /> 119 <param name="input_options_selector" value="vcf" />
120 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out6.vcf" /> 120 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out6.vcf" />