Mercurial > repos > iuc > bcftools_convert_to_vcf
diff bcftools_convert_to_vcf.xml @ 2:236f3634fb19 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2017 06:52:23 -0500 |
| parents | 5f1bb83e30f0 |
| children | dccf11c79157 |
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--- a/bcftools_convert_to_vcf.xml Wed Jul 13 10:50:35 2016 -0400 +++ b/bcftools_convert_to_vcf.xml Sat Jan 21 06:52:23 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"/>