Mercurial > repos > iuc > bcftools_convert_to_vcf
diff bcftools_convert_to_vcf.xml @ 3:d6e3d97e17f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
| author | iuc |
|---|---|
| date | Tue, 31 Jan 2017 12:42:27 -0500 |
| parents | b068ef999550 |
| children | 19167fd970a3 |
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--- a/bcftools_convert_to_vcf.xml Mon Oct 03 12:15:07 2016 -0400 +++ b/bcftools_convert_to_vcf.xml Tue Jan 31 12:42:27 2017 -0500 @@ -12,16 +12,16 @@ #set $input_vcf = None #if $convert.convert_from == 'gvcf': #set $input_vcf = 'input.vcf.gz' - #if $convert.input_file.datatype.file_ext == 'vcf' + #if $convert.input_file.is_of_type('vcf') bgzip -c "$convert.input_file" > $input_vcf && bcftools index $input_vcf && - #elif $convert.input_file.datatype.file_ext == 'vcf_bgzip' + #elif $convert.input_file.is_of_type('vcf_bgzip') ln -s "$convert.input_file" $input_vcf - #elif $convert.input_file.datatype.file_ext == 'bcf' + #elif $convert.input_file.is_of_type('bcf') #set $input_vcf = 'input.bcf' - ln -s "$convert.input_file" $input_vcf && + ln -s "$convert.input_file" $input_vcf && bcftools index $input_vcf && - #elif $convert.input_file.datatype.file_ext == 'bcf_bgzip' + #elif $convert.input_file.is_of_type('bcf_bgzip') ln -s "$convert.input_file" $input_vcf && #end if #end if @@ -61,7 +61,7 @@ <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option> </param> <when value="tsv"> - <param name="input_file" type="data" format="tabular" label="Tabular Variant Data" + <param name="input_file" type="data" format="tabular" label="Tabular Variant Data" help="Reference sequence and samples are required"/> <expand macro="macro_fasta_ref" /> <expand macro="macro_samples"/>