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fix for --variant-input in freebayes #6950

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fix for --variant-input in freebayes #6950

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6 changes: 2 additions & 4 deletions tools/freebayes/freebayes.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
## Tabixize optional input_variant_vcf file (for --variant-input option)
#if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
#end if

##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
Expand Down Expand Up @@ -365,9 +365,7 @@
<when value="do_not_provide" />
<when value="provide_vcf">
<param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
label="Use variants reported in this VCF dataset as input to the algorithm">
<conversion name="Tabixized_input" type="tabix" />
</param>
label="Use variants reported in this VCF dataset as input to the algorithm"/>
<param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
label="Only provide variant calls and genotype likelihoods for sites in VCF" />
</when>
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