Mercurial > repos > greg > bcftools_sort
diff macros.xml @ 0:1d4c51dcbbbe draft
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author | greg |
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date | Wed, 19 Dec 2018 08:58:27 -0500 |
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children | bb0f975d69b4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 19 08:58:27 2018 -0500 @@ -0,0 +1,92 @@ +<macros> + <token name="@VERSION@">1.4.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.9">bcftools</requirement> + <requirement type="package" version="1.9">htslib</requirement> + <yield /> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <yield /> + </citations> + </xml> + <token name="@THREADS@"> + --threads \${GALAXY_SLOTS:-4} + </token> + <token name="@PREPARE_ENV@"> +<![CDATA[ +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; +]]> + </token> + <xml name="macro_input"> + <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" /> + </xml> + <token name="@PREPARE_INPUT_FILE@"> +<![CDATA[ +## May need to symlink input if there is an associated +#set $input_vcf = 'input.vcf.gz' +#if $input_file.is_of_type('vcf') + bgzip -c '$input_file' > $input_vcf && + bcftools index $input_vcf && +#elif $input_file.is_of_type('vcf_bgzip') + ln -s '$input_file' $input_vcf && +#elif $input_file.is_of_type('bcf') + #set $input_vcf = 'input.bcf' + ln -s '$input_file' $input_vcf && + #if $input_file.metadata.bcf_index: + ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && + #else + bcftools index $input_vcf && + #end if +#elif $input_file.is_of_type('bcf_bgzip') + ln -s '$input_file' $input_vcf && +#end if +]]> + </token> + <token name="@INPUT_FILE@"> +$input_vcf + </token> + <xml name="macro_select_output_type"> + <param name="output_type" type="select"> + <option value="b">compressed BCF</option> + <option value="u">uncompressed BCF</option> + <option value="z">compressed VCF</option> + <option value="v">uncompressed VCF</option> + </param> + </xml> + <token name="@OUTPUT_TYPE@"> +#if str($output_type) != "__none__": + --output-type '${output_type}' +#end if + </token> + + <xml name="macro_vcf_output"> + <data name="output_file" format="vcf"> + <change_format> + <when input="output_type" value="b" format="bcf" /> + <when input="output_type" value="u" format="bcf" /> + <when input="output_type" value="z" format="vcf_bgzip" /> + <when input="output_type" value="v" format="vcf" /> + </change_format> + </data> + </xml> + + <token name="@OUTPUT_HELP@"> + <![CDATA[ +Output Type +----------- + +Output compressed BCF (b), or uncompressed VCF (v). +Use the BCF option when piping between bcftools subcommands to speed up +performance by removing unecessary compression/decompression +and VCF<->BCF conversion. + +This Galaxy tool recommends using the compressed BCF format +as piping is not implemented, and uncompressed data would +use unnecessary amounts of space. + ]]></token> +</macros> +