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comparison bcftools_convert_to_vcf.xml @ 0:b068ef999550 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:02:49 -0400
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children d6e3d97e17f0
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-1:000000000000 0:b068ef999550
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@.0">
3 <description>Converts other formats to VCF/BCFk</description>
4 <macros>
5 <token name="@EXECUTABLE@">convert</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 #set $input_vcf = None
13 #if $convert.convert_from == 'gvcf':
14 #set $input_vcf = 'input.vcf.gz'
15 #if $convert.input_file.datatype.file_ext == 'vcf'
16 bgzip -c "$convert.input_file" > $input_vcf &&
17 bcftools index $input_vcf &&
18 #elif $convert.input_file.datatype.file_ext == 'vcf_bgzip'
19 ln -s "$convert.input_file" $input_vcf
20 #elif $convert.input_file.datatype.file_ext == 'bcf'
21 #set $input_vcf = 'input.bcf'
22 ln -s "$convert.input_file" $input_vcf &&
23 bcftools index $input_vcf &&
24 #elif $convert.input_file.datatype.file_ext == 'bcf_bgzip'
25 ln -s "$convert.input_file" $input_vcf &&
26 #end if
27 #end if
28 #set $section = $convert
29 @PREPARE_FASTA_REF@
30
31 bcftools @EXECUTABLE@
32
33 @OUTPUT_TYPE@
34
35 #set $section = $convert
36 #if $convert.convert_from == 'gen_sample':
37 --gensample2vcf "$convert.input_file,$convert.input_sample"
38 #elif $convert.convert_from == 'hap_sample':
39 --hapsample2vcf "$convert.input_file,$convert.input_sample"
40 #elif $convert.convert_from == 'hap_legend_sample':
41 --haplegendsample2vcf "$convert.input_file,$convert.input_legend,$convert.input_sample"
42 #elif $convert.convert_from == 'gvcf':
43 @FASTA_REF@
44 --gvcf2vcf $input_vcf
45 #elif $convert.convert_from == 'tsv':
46 @FASTA_REF@
47 @SAMPLES@
48 @COLUMNS@
49 --tsv2vcf "$convert.input_file"
50 #end if
51 > "$output_file"
52 ]]>
53 </command>
54 <inputs>
55 <conditional name="convert">
56 <param name="convert_from" type="select" label="convert from">
57 <option value="tsv">tsv - TAB-Separated-Value (e.g. 23andMe)</option>
58 <option value="gvcf">gVCF - GATK Variant Call Format</option>
59 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
60 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option>
61 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option>
62 </param>
63 <when value="tsv">
64 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data"
65 help="Reference sequence and samples are required"/>
66 <expand macro="macro_fasta_ref" />
67 <expand macro="macro_samples"/>
68 <expand macro="macro_columns"/>
69 </when>
70 <when value="gvcf">
71 <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" />
72 <expand macro="macro_fasta_ref" />
73 </when>
74 <when value="gen_sample">
75 <param name="input_file" type="data" format="tabular" label="The .gen file" />
76 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
77 </when>
78 <when value="hap_sample">
79 <param name="input_file" type="data" format="tabular" label="The .hap file" />
80 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
81 </when>
82 <when value="hap_legend_sample">
83 <param name="input_file" type="data" format="tabular" label="The .hap file" />
84 <param name="input_legend" type="data" format="tabular" label="The .legend file" />
85 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
86 </when>
87
88 </conditional>
89 <expand macro="macro_select_output_type" />
90 </inputs>
91 <outputs>
92 <expand macro="macro_vcf_output"/>
93 </outputs>
94 <tests>
95 <test>
96 <param name="convert_from" value="gen_sample" />
97 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" />
98 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" />
99 <param name="output_type" value="v" />
100 <output name="output_file">
101 <assert_contents>
102 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
103 <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" />
104 </assert_contents>
105 </output>
106 </test>
107 <test>
108 <param name="convert_from" value="hap_sample" />
109 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" />
110 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" />
111 <param name="output_type" value="v" />
112 <output name="output_file">
113 <assert_contents>
114 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
115 <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" />
116 </assert_contents>
117 </output>
118 </test>
119 <test>
120 <param name="convert_from" value="hap_legend_sample" />
121 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" />
122 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" />
123 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" />
124 <param name="output_type" value="v" />
125 <output name="output_file">
126 <assert_contents>
127 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
128 <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" />
129 </assert_contents>
130 </output>
131 </test>
132 <test>
133 <param name="convert_from" value="gvcf" />
134 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" />
135 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" />
136 <param name="output_type" value="v" />
137 <output name="output_file">
138 <assert_contents>
139 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
140 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
141 </assert_contents>
142 </output>
143 </test>
144 <test>
145 <param name="convert_from" value="tsv" />
146 <param name="input_file" ftype="tabular" value="convert.23andme" />
147 <param name="fasta_ref" ftype="fasta" value="23andme.fa" />
148 <param name="samples" value="SAMPLE1" />
149 <param name="columns" value="ID,CHROM,POS,AA" />
150 <param name="output_type" value="v" />
151 <output name="output_file">
152 <assert_contents>
153 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
154 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
155 </assert_contents>
156 </output>
157 </test>
158 </tests>
159
160 <help><![CDATA[
161 =====================================
162 bcftools @EXECUTABLE@ plugin
163 =====================================
164
165 Converts other variant formats to vcf. See man page for file formats details.
166
167 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
168
169 @BCFTOOLS_WIKI@
170 ]]>
171 </help>
172 <expand macro="citations" />
173 </tool>