Mercurial > repos > iuc > bcftools_convert_to_vcf
diff bcftools_convert_to_vcf.xml @ 8:843e008b15fd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
| author | iuc |
|---|---|
| date | Wed, 05 Jun 2019 13:11:03 -0400 |
| parents | 367ba501b6eb |
| children | 8bb5efd7a3dd |
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--- a/bcftools_convert_to_vcf.xml Thu Feb 21 16:05:01 2019 -0500 +++ b/bcftools_convert_to_vcf.xml Wed Jun 05 13:11:03 2019 -0400 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@+galaxy1"> <description>Converts other formats to VCF/BCFk</description> <macros> <token name="@EXECUTABLE@">convert</token> @@ -27,14 +27,15 @@ ln -s '$convert.input_file' $input_vcf && #end if #end if -#set $section = $convert -@PREPARE_FASTA_REF@ +#if $convert.convert_from == 'gvcf' or $convert.convert_from == 'tsv': + #set $section = $convert.reference_source + @PREPARE_FASTA_REF@ +#end if bcftools @EXECUTABLE@ @OUTPUT_TYPE@ -#set $section = $convert #if $convert.convert_from == 'gen_sample': --gensample2vcf '$convert.input_file,$convert.input_sample' #elif $convert.convert_from == 'hap_sample': @@ -46,6 +47,7 @@ --gvcf2vcf $input_vcf #elif $convert.convert_from == 'tsv': @FASTA_REF@ + #set $section = $convert @SAMPLES@ @COLUMNS@ --tsv2vcf '$convert.input_file' @@ -95,9 +97,11 @@ </outputs> <tests> <test> - <param name="convert_from" value="gen_sample" /> - <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" /> - <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" /> + <conditional name="convert"> + <param name="convert_from" value="gen_sample" /> + <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" /> + <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" /> + </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -107,9 +111,26 @@ </output> </test> <test> - <param name="convert_from" value="hap_sample" /> - <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" /> - <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" /> + <conditional name="convert"> + <param name="convert_from" value="hap_sample" /> + <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" /> + <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" /> + </conditional> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> + <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="convert"> + <param name="convert_from" value="hap_legend_sample" /> + <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" /> + <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" /> + <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" /> + </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -119,22 +140,11 @@ </output> </test> <test> - <param name="convert_from" value="hap_legend_sample" /> - <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" /> - <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" /> - <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" /> - <param name="output_type" value="v" /> - <output name="output_file"> - <assert_contents> - <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> - <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" /> - </assert_contents> - </output> - </test> - <test> - <param name="convert_from" value="gvcf" /> - <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" /> - <param name="fasta_ref" ftype="fasta" value="gvcf.fa" /> + <conditional name="convert"> + <param name="convert_from" value="gvcf" /> + <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" /> + <expand macro="test_using_reference" ref="gvcf.fa" /> + </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -144,11 +154,43 @@ </output> </test> <test> - <param name="convert_from" value="tsv" /> - <param name="input_file" ftype="tabular" value="convert.23andme" /> - <param name="fasta_ref" ftype="fasta" value="23andme.fa" /> - <param name="samples" value="SAMPLE1" /> - <param name="columns" value="ID,CHROM,POS,AA" /> + <conditional name="convert"> + <param name="convert_from" value="gvcf" /> + <param name="input_file" ftype="vcf" dbkey="?" value="convert.gvcf.vcf" /> + <expand macro="test_using_reference" select_from="cached" ref="gvcf" /> + </conditional> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> + <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="convert"> + <param name="convert_from" value="tsv" /> + <param name="input_file" ftype="tabular" value="convert.23andme" /> + <expand macro="test_using_reference" ref="23andme.fa" /> + <param name="samples" value="SAMPLE1" /> + <param name="columns" value="ID,CHROM,POS,AA" /> + </conditional> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" /> + <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="convert"> + <param name="convert_from" value="tsv" /> + <param name="input_file" ftype="tabular" dbkey="?" value="convert.23andme" /> + <expand macro="test_using_reference" select_from="cached" ref="23andme" /> + <param name="samples" value="SAMPLE1" /> + <param name="columns" value="ID,CHROM,POS,AA" /> + </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents>