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comparison beagle.xml @ 2:ab97b3b44590 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
author iuc
date Sat, 03 May 2025 11:38:34 +0000
parents d0a6954d0a0a
children d93346789db9
comparison
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1:d0a6954d0a0a 2:ab97b3b44590
1 <tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'> 1 <tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='23.0'>
2 <description>phasing genotypes and imputing ungenotyped markers</description> 2 <description>phasing genotypes and imputing ungenotyped markers</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
8 <command detect_errors='exit_code'><![CDATA[ 8 <command detect_errors='exit_code'><![CDATA[
9 #set out_prefix='out' 9 #set out_prefix='out'
10 #if $optional_inputs.ref 10 #if $optional_inputs.ref
11 ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext && 11 ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
12 #end if 12 #end if
13 13 #if $gt.ext=="vcf_bgzip"
14 ln -s '$gt' tmp.gz &&
15 #end if
14 beagle 16 beagle
15 gt='${gt}' 17 #if $gt.ext=="vcf_bgzip"
18 gt=tmp.gz
19 #else
20 gt='${gt}'
21 #end if
16 #if $optional_inputs.ref 22 #if $optional_inputs.ref
17 ref=ref.$optional_inputs.ref.ext 23 ref=ref.$optional_inputs.ref.ext
18 #end if 24 #end if
19 #if $optional_inputs.map 25 #if $optional_inputs.map
20 map='${optional_inputs.map}' 26 map='${optional_inputs.map}'
47 cluster=$imputation_parameters.cluster 53 cluster=$imputation_parameters.cluster
48 ap=$imputation_parameters.ap 54 ap=$imputation_parameters.ap
49 gp=$imputation_parameters.gp 55 gp=$imputation_parameters.gp
50 out=$out_prefix 56 out=$out_prefix
51 nthreads=\${GALAXY_SLOTS:-1} 57 nthreads=\${GALAXY_SLOTS:-1}
52 && gunzip 'out.vcf.gz' 58 #if $out_format == "vcf_bgzip"
59 && mv out.vcf.gz '$vcf_file'
60 #else
61 && echo "decompressing beagle output"
62 && gunzip 'out.vcf.gz'
63 && mv out.vcf '$vcf_file'
64 #end if
53 ]]> </command> 65 ]]> </command>
54 <inputs> 66 <inputs>
55 <param argument="gt" type="data" format="vcf" label="VCF file" 67 <param argument="gt" type="data" format="vcf" label="VCF file"
56 help="It specifies a VCF file containing genotypes for the study samples. 68 help="It specifies a VCF file containing genotypes for the study samples.
57 Each VCF record must contain a GT (genotype) format field"/> 69 Each VCF record must contain a GT (genotype) format field"/>
133 probabilities assuming Hardy-Weinberg Equilibrium. Consequently, the alleles in the genotype 145 probabilities assuming Hardy-Weinberg Equilibrium. Consequently, the alleles in the genotype
134 with highest genotype probability may occasionally be different than the genotype obtained by 146 with highest genotype probability may occasionally be different than the genotype obtained by
135 taking the allele with highest probability on each haplotype, which is the genotype reported 147 taking the allele with highest probability on each haplotype, which is the genotype reported
136 in the GT format field" /> 148 in the GT format field" />
137 </section> 149 </section>
150 <param name="out_format" type="select" label="Output data type ">
151 <option value="vcf" selected="true">VCF</option>
152 <option value="vcf_bgzip">Compressed VCF (bgzip)</option>
153 </param>
138 </inputs> 154 </inputs>
139 <outputs> 155 <outputs>
140 <data name="vcf_file" format="vcf" from_work_dir="out.vcf" label="${tool.name} on ${on_string}: VCF file"/> 156 <data name="vcf_file" format="vcf" label="${tool.name} on ${on_string}: VCF file">
157 <change_format>
158 <when input="out_format" value="vcf_bgzip" format="vcf_bgzip" />
159 </change_format>
160 </data>
141 <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file"> 161 <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file">
142 <filter>output_log</filter> 162 <filter>output_log</filter>
143 </data> 163 </data>
144 </outputs> 164 </outputs>
145 <tests> 165 <tests>
181 <param name="phase_states" value="250"/> 201 <param name="phase_states" value="250"/>
182 </section> 202 </section>
183 <output name="vcf_file" ftype="vcf"> 203 <output name="vcf_file" ftype="vcf">
184 <assert_contents> 204 <assert_contents>
185 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/> 205 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
186 <has_size value="181272"/> 206 <has_size value="181410"/>
187 </assert_contents> 207 </assert_contents>
188 </output> 208 </output>
189 <output name="log_file" ftype="txt"> 209 <output name="log_file" ftype="txt">
190 <assert_contents> 210 <assert_contents>
191 <has_text text="Reference markers: 223"/> 211 <has_text text="Study markers: 223"/>
192 <has_size value="1586" delta="100"/> 212 <has_size value="1696" delta="100"/>
193 <has_text text="WARNING" negate="true"/> 213 <has_text text="WARNING" negate="true"/>
194 <has_text_matching expression="beagle.*jar finished"/> 214 <has_text_matching expression="beagle.*jar finished"/>
195 </assert_contents> 215 </assert_contents>
196 </output> 216 </output>
197 </test> 217 </test>
215 <param name="gp" value="true"/> 235 <param name="gp" value="true"/>
216 </section> 236 </section>
217 <output name="vcf_file" ftype="vcf"> 237 <output name="vcf_file" ftype="vcf">
218 <assert_contents> 238 <assert_contents>
219 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/> 239 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
220 <has_size value="18635"/> 240 <has_size value="18773"/>
221 </assert_contents> 241 </assert_contents>
222 </output> 242 </output>
223 <output name="log_file" ftype="txt"> 243 <output name="log_file" ftype="txt">
224 <assert_contents> 244 <assert_contents>
225 <has_text text="Reference markers: 223"/> 245 <has_text text="Reference markers: 223"/>
226 <has_size value="1600" delta="100"/> 246 <has_size value="1754" delta="100"/>
227 <has_text text="WARNING" negate="true"/> 247 <has_text text="WARNING" negate="true"/>
228 <has_text_matching expression="beagle.*jar finished"/> 248 <has_text_matching expression="beagle.*jar finished"/>
229 </assert_contents> 249 </assert_contents>
230 </output> 250 </output>
231 </test> 251 </test>
248 <param name="gp" value="true"/> 268 <param name="gp" value="true"/>
249 </section> 269 </section>
250 <output name="vcf_file" ftype="vcf"> 270 <output name="vcf_file" ftype="vcf">
251 <assert_contents> 271 <assert_contents>
252 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/> 272 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
253 <has_size value="18635"/> 273 <has_size value="18773"/>
254 </assert_contents> 274 </assert_contents>
255 </output> 275 </output>
276 </test>
277 <!-- Test vcf_bgzip output -->
278 <test expect_num_outputs="1">
279 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
280 <param name="chrom" value="22:100-"/>
281 <param name="ne" value="1000000"/>
282 <param name="window" value="40.0"/>
283 <param name="overlap" value="2.0"/>
284 <param name="err" value="0.02"/>
285 <param name="seed" value="1"/>
286 <section name="phasing_parameters">
287 <param name="burnin" value="3"/>
288 <param name="iterations" value="12"/>
289 <param name="phase_states" value="280"/>
290 </section>
291 <param name="out_format" value="vcf_bgzip"/>
292 <output name="vcf_file" ftype="vcf_bgzip" file="test_output.vcf.gz" compare="sim_size" delta="500"/>
293
256 </test> 294 </test>
257 </tests> 295 </tests>
258 <help><![CDATA[ 296 <help><![CDATA[
259 .. class:: infomark 297 .. class:: infomark
260 298