Mercurial > repos > scisjnu123 > ngsap_vc
diff ngsap-vc/gatk/combine_gvcfs.xml @ 3:0d10255b5434 draft default tip
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author | scisjnu123 |
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date | Thu, 03 Oct 2019 10:42:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngsap-vc/gatk/combine_gvcfs.xml Thu Oct 03 10:42:15 2019 -0400 @@ -0,0 +1,44 @@ +<macros> + <xml name="CombineGVCFsParameters" tokens="tag"> + + <expand macro="macro_gvcf_input" tag="@TAG@" /> + + <expand macro="macro_optional_parameters"> + + <param name="breakBandsAtMultiplesOf" type="integer" value="0" label="If > 0, reference bands will be broken up at genomic positions that are multiples of this number" help="-breakBandsAtMultiplesOf,‑‑breakBandsAtMultiplesOf &lt;breakBandsAtMultiplesOf&gt;" /> + + </expand> + + </xml> + + <xml name="CombineGVCFsOutput"> + <data format="vcf" name="cg_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)"> + <yield /> + </data> + </xml> + + <template name="CombineGVCFsPreprocessing"> +<![CDATA[ + @token_gvcf_input_pre@ +]]> + </template> + + <template name="CombineGVCFsOptions"> +<![CDATA[ + --out ${cg_output_vcf} + + @token_gvcf_input@ + + #set $optionals = $analysis_type.optional_parameters + #if $optionals.optional_parameters_enabled + #if $optionals.breakBandsAtMultiplesOf > 0 + --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf + #end if + #end if +]]> + </template> + + +</macros> + +