Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison bcftools_convert_to_vcf.xml @ 8:843e008b15fd draft

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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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7:367ba501b6eb 8:843e008b15fd
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@+galaxy1">
3 <description>Converts other formats to VCF/BCFk</description> 3 <description>Converts other formats to VCF/BCFk</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">convert</token> 5 <token name="@EXECUTABLE@">convert</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
25 bcftools index $input_vcf && 25 bcftools index $input_vcf &&
26 #elif $convert.input_file.is_of_type('bcf_bgzip') 26 #elif $convert.input_file.is_of_type('bcf_bgzip')
27 ln -s '$convert.input_file' $input_vcf && 27 ln -s '$convert.input_file' $input_vcf &&
28 #end if 28 #end if
29 #end if 29 #end if
30 #set $section = $convert 30 #if $convert.convert_from == 'gvcf' or $convert.convert_from == 'tsv':
31 @PREPARE_FASTA_REF@ 31 #set $section = $convert.reference_source
32 @PREPARE_FASTA_REF@
33 #end if
32 34
33 bcftools @EXECUTABLE@ 35 bcftools @EXECUTABLE@
34 36
35 @OUTPUT_TYPE@ 37 @OUTPUT_TYPE@
36 38
37 #set $section = $convert
38 #if $convert.convert_from == 'gen_sample': 39 #if $convert.convert_from == 'gen_sample':
39 --gensample2vcf '$convert.input_file,$convert.input_sample' 40 --gensample2vcf '$convert.input_file,$convert.input_sample'
40 #elif $convert.convert_from == 'hap_sample': 41 #elif $convert.convert_from == 'hap_sample':
41 --hapsample2vcf '$convert.input_file,$convert.input_sample' 42 --hapsample2vcf '$convert.input_file,$convert.input_sample'
42 #elif $convert.convert_from == 'hap_legend_sample': 43 #elif $convert.convert_from == 'hap_legend_sample':
44 #elif $convert.convert_from == 'gvcf': 45 #elif $convert.convert_from == 'gvcf':
45 @FASTA_REF@ 46 @FASTA_REF@
46 --gvcf2vcf $input_vcf 47 --gvcf2vcf $input_vcf
47 #elif $convert.convert_from == 'tsv': 48 #elif $convert.convert_from == 'tsv':
48 @FASTA_REF@ 49 @FASTA_REF@
50 #set $section = $convert
49 @SAMPLES@ 51 @SAMPLES@
50 @COLUMNS@ 52 @COLUMNS@
51 --tsv2vcf '$convert.input_file' 53 --tsv2vcf '$convert.input_file'
52 #end if 54 #end if
53 > '$output_file' 55 > '$output_file'
93 <outputs> 95 <outputs>
94 <expand macro="macro_vcf_output"/> 96 <expand macro="macro_vcf_output"/>
95 </outputs> 97 </outputs>
96 <tests> 98 <tests>
97 <test> 99 <test>
98 <param name="convert_from" value="gen_sample" /> 100 <conditional name="convert">
99 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" /> 101 <param name="convert_from" value="gen_sample" />
100 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" /> 102 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" />
103 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" />
104 </conditional>
101 <param name="output_type" value="v" /> 105 <param name="output_type" value="v" />
102 <output name="output_file"> 106 <output name="output_file">
103 <assert_contents> 107 <assert_contents>
104 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> 108 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
105 <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" /> 109 <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" />
106 </assert_contents> 110 </assert_contents>
107 </output> 111 </output>
108 </test> 112 </test>
109 <test> 113 <test>
110 <param name="convert_from" value="hap_sample" /> 114 <conditional name="convert">
111 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" /> 115 <param name="convert_from" value="hap_sample" />
112 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" /> 116 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" />
117 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" />
118 </conditional>
113 <param name="output_type" value="v" /> 119 <param name="output_type" value="v" />
114 <output name="output_file"> 120 <output name="output_file">
115 <assert_contents> 121 <assert_contents>
116 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> 122 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
117 <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" /> 123 <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" />
118 </assert_contents> 124 </assert_contents>
119 </output> 125 </output>
120 </test> 126 </test>
121 <test> 127 <test>
122 <param name="convert_from" value="hap_legend_sample" /> 128 <conditional name="convert">
123 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" /> 129 <param name="convert_from" value="hap_legend_sample" />
124 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" /> 130 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" />
125 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" /> 131 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" />
132 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" />
133 </conditional>
126 <param name="output_type" value="v" /> 134 <param name="output_type" value="v" />
127 <output name="output_file"> 135 <output name="output_file">
128 <assert_contents> 136 <assert_contents>
129 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> 137 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
130 <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" /> 138 <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" />
131 </assert_contents> 139 </assert_contents>
132 </output> 140 </output>
133 </test> 141 </test>
134 <test> 142 <test>
135 <param name="convert_from" value="gvcf" /> 143 <conditional name="convert">
136 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" /> 144 <param name="convert_from" value="gvcf" />
137 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" /> 145 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" />
146 <expand macro="test_using_reference" ref="gvcf.fa" />
147 </conditional>
138 <param name="output_type" value="v" /> 148 <param name="output_type" value="v" />
139 <output name="output_file"> 149 <output name="output_file">
140 <assert_contents> 150 <assert_contents>
141 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> 151 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
142 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> 152 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
143 </assert_contents> 153 </assert_contents>
144 </output> 154 </output>
145 </test> 155 </test>
146 <test> 156 <test>
147 <param name="convert_from" value="tsv" /> 157 <conditional name="convert">
148 <param name="input_file" ftype="tabular" value="convert.23andme" /> 158 <param name="convert_from" value="gvcf" />
149 <param name="fasta_ref" ftype="fasta" value="23andme.fa" /> 159 <param name="input_file" ftype="vcf" dbkey="?" value="convert.gvcf.vcf" />
150 <param name="samples" value="SAMPLE1" /> 160 <expand macro="test_using_reference" select_from="cached" ref="gvcf" />
151 <param name="columns" value="ID,CHROM,POS,AA" /> 161 </conditional>
162 <param name="output_type" value="v" />
163 <output name="output_file">
164 <assert_contents>
165 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
166 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
167 </assert_contents>
168 </output>
169 </test>
170 <test>
171 <conditional name="convert">
172 <param name="convert_from" value="tsv" />
173 <param name="input_file" ftype="tabular" value="convert.23andme" />
174 <expand macro="test_using_reference" ref="23andme.fa" />
175 <param name="samples" value="SAMPLE1" />
176 <param name="columns" value="ID,CHROM,POS,AA" />
177 </conditional>
178 <param name="output_type" value="v" />
179 <output name="output_file">
180 <assert_contents>
181 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
182 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
183 </assert_contents>
184 </output>
185 </test>
186 <test>
187 <conditional name="convert">
188 <param name="convert_from" value="tsv" />
189 <param name="input_file" ftype="tabular" dbkey="?" value="convert.23andme" />
190 <expand macro="test_using_reference" select_from="cached" ref="23andme" />
191 <param name="samples" value="SAMPLE1" />
192 <param name="columns" value="ID,CHROM,POS,AA" />
193 </conditional>
152 <param name="output_type" value="v" /> 194 <param name="output_type" value="v" />
153 <output name="output_file"> 195 <output name="output_file">
154 <assert_contents> 196 <assert_contents>
155 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" /> 197 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
156 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" /> 198 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />