Mercurial > repos > artbio > gatk4
comparison FilterMutectCalls.xml @ 2:646e6943bcd2 draft default tip
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 |
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| 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" /> |