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comparison bcftools_view.xml @ 16:bb21cedd0dc9 draft

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author wrtz
date Thu, 14 Jan 2016 17:51:20 -0500
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15:9d96f73b875f 16:bb21cedd0dc9
1 <tool id="bcftools_view" name="BCFtools view" version="1.0.0">
2 <description>Convert, view, subset, and filter VCF/BCF files</description>
3 <command>
4 #if str( $input_file_index ) != "None":
5 ln -s -f $input input_file.${input.ext} &amp;&amp;
6 ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
7 #end if
8 bcftools view
9 ${drop_genotypes}
10 ${header_only}
11 ${no_header}
12 --output-file "${output_file}"
13 --output-type "${output_type}"
14 #if str( $regions ) != "":
15 --regions "${regions}"
16 #end if
17 #if str( $targets ) != "":
18 --targets "${targets}"
19 #end if
20 #if str( $samples ) != "":
21 --samples "${samples}"
22 #end if
23 #if str( $regions_file ) != "None":
24 --regions-file "${regions_file}"
25 #end if
26 #if str( $targets_file ) != "None":
27 --targets-file "${targets_file}"
28 #end if
29 #if str( $samples_file ) != "None":
30 --samples-file "${samples_file}"
31 #end if
32 #if str( $apply_filters ) != "":
33 --apply-filters "${apply_filters}"
34 #end if
35 #if str( $min_ac_cond.set_min_ac ) == "True":
36 --min-ac $min_ac_cond.min_ac:$min_ac_cond.min_ac_type
37 #end if
38 #if str( $max_ac_cond.set_max_ac ) == "True":
39 --max-ac $max_ac_cond.max_ac:$max_ac_cond.max_ac_type
40 #end if
41 #if str( $min_af_cond.set_min_af ) == "True":
42 --min-af $min_af_cond.min_af:$min_af_cond.min_af_type
43 #end if
44 #if str( $max_af_cond.set_max_af ) == "True":
45 --max-af $max_af_cond.max_af:$max_af_cond.max_af_type
46 #end if
47 #if str( $expr_cond.set_expr ) == "True":
48 #if str( $expr_cond.include_or_exclude ) == "include":
49 --include "${expr_cond.expr}"
50 #else
51 --exclude "${expr_cond.expr}"
52 #end if
53 #end if
54 #if str( $genotype_cond.set_genotype ) == "True":
55 #if str( $genotype_cond.include_or_exclude ) == "include":
56 --genotype $genotype_cond.genotype
57 #else
58 --genotype ^$genotype_cond.genotype
59 #end if
60 #end if
61 #if str( $var_type_cond.set_var_type ) == "True":
62 #if str( $var_type_cond.include_or_exclude ) == "include":
63 --types $var_type_cond.var_types
64 #else
65 --exclude-types $var_type_cond.var_types
66 #end if
67 #end if
68 ${uncalled}
69 ${exclude_uncalled}
70 ${private}
71 ${exclude_private}
72
73 #if str( $input_file_index ) != "None":
74 input_file.${input.ext}
75 #else
76 $input
77 #end if
78 </command>
79
80 <inputs>
81 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
82 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
83 <param name="output_type" type="select" label="Output data type" help="-O">
84 <option value="v" selected="true">VCF</option>
85 <option value="b">BCF</option>
86 </param>
87 <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
88 <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
89 <sanitizer invalid_char="">
90 <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
91 </sanitizer>
92 </param>
93 <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
94 <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
95 <sanitizer invalid_char="">
96 <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
97 </sanitizer>
98 </param>
99 <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
100 <param name="samples" type="text" size="80" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
101 <param name="apply_filters" type="text" size="80" optional="True" label="Apply filters" help="-f. Comma-separated list of strings. Keeps only sites where FILTER column contains one of these strings." />
102 <param name="drop_genotypes" type="boolean" checked="False" truevalue="--drop-genotypes" falsevalue="" label="Drop individual genotype information" help="-G" />
103 <param name="no_header" type="boolean" checked="False" truevalue="--no-header" falsevalue="" label="Suppress the header in VCF output" help="-H" />
104 <param name="header_only" type="boolean" checked="False" truevalue="--header-only" falsevalue="" label="Output the VCF header only" help="-h" />
105 <conditional name="min_ac_cond">
106 <param name="set_min_ac" type="boolean" checked="False" label="Set minimum allele count" help="-c" />
107 <when value="true">
108 <param name="min_ac" type="integer" optional="true" label="Minimum allele count" help="Minimum allele count of sites to be printed, for given allele type." />
109 <param name="min_ac_type" type="select" label="Allele type">
110 <option value="nref" selected="True">Non-reference</option>
111 <option value="alt1">1st alternate</option>
112 <option value="minor">Minor (least frequent)</option>
113 <option value="major">Major (most frequent)</option>
114 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
115 </param>
116 </when>
117 </conditional>
118 <conditional name="max_ac_cond">
119 <param name="set_max_ac" type="boolean" checked="False" label="Set maximum allele count" help="-C" />
120 <when value="true">
121 <param name="max_ac" type="integer" optional="true" label="Maximum allele count" help="Maximum allele count of sites to be printed, for given allele type." />
122 <param name="max_ac_type" type="select" label="Allele type">
123 <option value="nref" selected="True">Non-reference</option>
124 <option value="alt1">1st alternate</option>
125 <option value="minor">Minor (least frequent)</option>
126 <option value="major">Major (most frequent)</option>
127 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
128 </param>
129 </when>
130 </conditional>
131
132 <conditional name="min_af_cond">
133 <param name="set_min_af" type="boolean" checked="False" label="Set minimum allele frequency" help="-q" />
134 <when value="true">
135 <param name="min_af" type="integer" optional="true" label="Minimum allele frequency" help="Minimum allele frequency of sites to be printed, for given allele type." />
136 <param name="min_af_type" type="select" label="Allele type">
137 <option value="nref" selected="True">Non-reference</option>
138 <option value="alt1">1st alternate</option>
139 <option value="minor">Minor (least frequent)</option>
140 <option value="major">Major (most frequent)</option>
141 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
142 </param>
143 </when>
144 </conditional>
145 <conditional name="max_af_cond">
146 <param name="set_max_af" type="boolean" checked="False" label="Set maximum allele frequency" help="-Q" />
147 <when value="true">
148 <param name="max_af" type="integer" optional="true" label="Maximum allele frequency" help="Maximum allele frequency of sites to be printed, for given allele type." />
149 <param name="max_af_type" type="select" label="Allele type">
150 <option value="nref" selected="True">Non-reference</option>
151 <option value="alt1">1st alternate</option>
152 <option value="minor">Minor (least frequent)</option>
153 <option value="major">Major (most frequent)</option>
154 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
155 </param>
156 </when>
157 </conditional>
158
159 <conditional name="genotype_cond">
160 <param name="set_genotype" type="boolean" checked="False" label="Filter by genotype" help="-g. Include only, or exclude, sites with one or more of given genotype."/>
161 <when value="true">
162 <param name="include_or_exclude" type="select" label="Include or exclude by genotype">
163 <option value="include">Include</option>
164 <option value="exclude">Exclude</option>
165 </param>
166 <param name="genotype" type="select" label="Genotype">
167 <option value="hom">Homozygous</option>
168 <option value="het">Heterozygous</option>
169 <option value="miss">Missing</option>
170 </param>
171 </when>
172 </conditional>
173
174 <conditional name="expr_cond">
175 <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/>
176 <when value="true">
177 <param name="include_or_exclude" type="select" label="Include or exclude by expression">
178 <option value="include">Include</option>
179 <option value="exclude">Exclude</option>
180 </param>
181 <param name="expr" type="text" size="80" label="Expression">
182 <sanitizer invalid_char="">
183 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
184 </sanitizer>
185 </param>
186 </when>
187 </conditional>
188
189 <conditional name="var_type_cond">
190 <param name="set_var_type" type="boolean" checked="False" label="Filter by variant type" help="-v, -V. Include/ exclude sites where any ALT allele is one of the given variant types."/>
191 <when value="true">
192 <param name="include_or_exclude" type="select" label="Include or exclude by variant type">
193 <option value="include">Include</option>
194 <option value="exclude">Exclude</option>
195 </param>
196 <param name="var_types" type="select" multiple="true" display="checkboxes" label="Variant type">
197 <option value="snps">SNPs</option>
198 <option value="indels">Indels</option>
199 <option value="mnps">MNPs</option>
200 <option value="other">Other</option>
201 </param>
202 </when>
203 </conditional>
204
205 <param name="uncalled" type="boolean" checked="False" truevalue="--uncalled" falsevalue="" label="Print sites without a called genotype" help="-u" />
206 <param name="exclude_uncalled" type="boolean" checked="False" truevalue="--exclude-uncalled" falsevalue="" label="Exclude sites without a called genotype" help="-U" />
207 <param name="private" type="boolean" checked="False" truevalue="--private" falsevalue="" label="Print sites where only the subset samples carry a non-reference allele" help="-x. Requires samples file or samples list."/>
208 <param name="exclude_private" type="boolean" checked="False" truevalue="--exclude-private" falsevalue="" label="Exclude sites where only the subset samples carry a non-reference allele" help="-X. Requires samples file or samples list."/>
209 </inputs>
210 <outputs>
211 <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
212 <change_format>
213 <when input="output_type" value="b" format="bcf" />
214 </change_format>
215 </data>
216 </outputs>
217 <help>
218 **About this tool**
219
220 **BCFtools view**: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF. Former bcftools subset.
221
222 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
223 </help>
224 </tool>