Mercurial > repos > iuc > beagle
comparison beagle.xml @ 1:f75bf16ac901 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
author | iuc |
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date | Sun, 22 Jan 2023 12:42:41 +0000 |
parents | 553b27c30eb8 |
children |
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0:553b27c30eb8 | 1:f75bf16ac901 |
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5 </macros> | 5 </macros> |
6 <expand macro='edam_ontology' /> | 6 <expand macro='edam_ontology' /> |
7 <expand macro='requirements' /> | 7 <expand macro='requirements' /> |
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.ext == 'bref3' | 10 #if $optional_inputs.ref |
11 ln -s '${optional_inputs.ref}' ref.bref3 && | 11 ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext && |
12 #end if | 12 #end if |
13 | |
13 beagle | 14 beagle |
14 gt='${gt}' | 15 gt='${gt}' |
15 #if $optional_inputs.ref and $optional_inputs.ref.ext == 'bref3' | 16 #if $optional_inputs.ref |
16 ref=ref.bref3 | 17 ref=ref.$optional_inputs.ref.ext |
17 #else if $optional_inputs.ref | |
18 ref='${optional_inputs.ref}' | |
19 #end if | 18 #end if |
20 #if $optional_inputs.map | 19 #if $optional_inputs.map |
21 map='${optional_inputs.map}' | 20 map='${optional_inputs.map}' |
22 #end if | 21 #end if |
23 #if $chrom | 22 #if $chrom |
144 </data> | 143 </data> |
145 </outputs> | 144 </outputs> |
146 <tests> | 145 <tests> |
147 <!-- Test default values --> | 146 <!-- Test default values --> |
148 <test expect_num_outputs="2"> | 147 <test expect_num_outputs="2"> |
149 <param name="gt" value="test.vcf.gz"/> | 148 <param name="gt" value="test.vcf.gz" ftype="vcf"/> |
150 <param name="chrom" value="22:100-"/> | 149 <param name="chrom" value="22:100-"/> |
151 <param name="ne" value="1000000"/> | 150 <param name="ne" value="1000000"/> |
152 <param name="window" value="40.0"/> | 151 <param name="window" value="40.0"/> |
153 <param name="overlap" value="2.0"/> | 152 <param name="overlap" value="2.0"/> |
154 <param name="err" value="0.02"/> | 153 <param name="err" value="0.02"/> |
158 <param name="burnin" value="3"/> | 157 <param name="burnin" value="3"/> |
159 <param name="iterations" value="12"/> | 158 <param name="iterations" value="12"/> |
160 <param name="phase_states" value="280"/> | 159 <param name="phase_states" value="280"/> |
161 </section> | 160 </section> |
162 <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/> | 161 <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/> |
163 <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"/> | 162 <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"> |
163 <assert_contents> | |
164 <has_text text="WARNING" negate="true"/> | |
165 </assert_contents> | |
166 </output> | |
164 </test> | 167 </test> |
165 <!-- Test plink file--> | 168 <!-- Test plink file--> |
166 <test expect_num_outputs="2"> | 169 <test expect_num_outputs="2"> |
167 <param name="gt" value="test.vcf.gz"/> | 170 <param name="gt" value="test.vcf.gz" ftype="vcf"/> |
168 <param name="ne" value="1000000"/> | 171 <param name="ne" value="1000000"/> |
169 <param name="window" value="30.0"/> | 172 <param name="window" value="30.0"/> |
170 <param name="overlap" value="3.0"/> | 173 <param name="overlap" value="3.0"/> |
171 <param name="output_log" value="true"/> | 174 <param name="output_log" value="true"/> |
172 <section name="optional_inputs"> | 175 <section name="optional_inputs"> |
184 </assert_contents> | 187 </assert_contents> |
185 </output> | 188 </output> |
186 <output name="log_file" ftype="txt"> | 189 <output name="log_file" ftype="txt"> |
187 <assert_contents> | 190 <assert_contents> |
188 <has_text text="Reference markers: 223"/> | 191 <has_text text="Reference markers: 223"/> |
189 <has_size value="1586" delta="10"/> | 192 <has_size value="1586" delta="100"/> |
193 <has_text text="WARNING" negate="true"/> | |
194 <has_text_matching expression="beagle.*jar finished"/> | |
190 </assert_contents> | 195 </assert_contents> |
191 </output> | 196 </output> |
192 </test> | 197 </test> |
193 <!-- Test ref VCF input --> | 198 <!-- Test ref VCF input --> |
194 <test expect_num_outputs="2"> | 199 <test expect_num_outputs="2"> |
195 <param name="gt" value="target.vcf.gz"/> | 200 <param name="gt" value="target.vcf.gz" ftype="vcf"/> |
196 <param name="ne" value="1000000"/> | 201 <param name="ne" value="1000000"/> |
197 <param name="window" value="40.0"/> | 202 <param name="window" value="40.0"/> |
198 <param name="overlap" value="2.0"/> | 203 <param name="overlap" value="2.0"/> |
199 <param name="output_log" value="true"/> | 204 <param name="output_log" value="true"/> |
200 <section name="optional_inputs"> | 205 <section name="optional_inputs"> |
201 <param name="ref" value="ref.vcf.gz"/> | 206 <param name="ref" value="ref.vcf.gz" ftype="vcf"/> |
202 </section> | 207 </section> |
203 <section name="imputation_parameters"> | 208 <section name="imputation_parameters"> |
204 <param name="impute" value="true"/> | 209 <param name="impute" value="true"/> |
205 <param name="imp_states" value="1600"/> | 210 <param name="imp_states" value="1600"/> |
206 <param name="imp_segment" value="6.0"/> | 211 <param name="imp_segment" value="6.0"/> |
216 </assert_contents> | 221 </assert_contents> |
217 </output> | 222 </output> |
218 <output name="log_file" ftype="txt"> | 223 <output name="log_file" ftype="txt"> |
219 <assert_contents> | 224 <assert_contents> |
220 <has_text text="Reference markers: 223"/> | 225 <has_text text="Reference markers: 223"/> |
221 <has_size value="1801" delta="10"/> | 226 <has_size value="1600" delta="100"/> |
227 <has_text text="WARNING" negate="true"/> | |
228 <has_text_matching expression="beagle.*jar finished"/> | |
222 </assert_contents> | 229 </assert_contents> |
223 </output> | 230 </output> |
224 </test> | 231 </test> |
225 <!-- Test ref bref3 input --> | 232 <!-- Test ref bref3 input --> |
226 <test expect_num_outputs="1"> | 233 <test expect_num_outputs="1"> |
227 <param name="gt" value="target.vcf.gz"/> | 234 <param name="gt" value="target.vcf.gz" ftype="vcf"/> |
228 <param name="ne" value="1000000"/> | 235 <param name="ne" value="1000000"/> |
229 <param name="window" value="40.0"/> | 236 <param name="window" value="40.0"/> |
230 <param name="overlap" value="2.0"/> | 237 <param name="overlap" value="2.0"/> |
231 <section name="optional_inputs"> | 238 <section name="optional_inputs"> |
232 <param name="ref" value="ref.bref3"/> | 239 <param name="ref" value="ref.bref3" ftype="bref3"/> |
233 </section> | 240 </section> |
234 <section name="imputation_parameters"> | 241 <section name="imputation_parameters"> |
235 <param name="impute" value="true"/> | 242 <param name="impute" value="true"/> |
236 <param name="imp_states" value="1600"/> | 243 <param name="imp_states" value="1600"/> |
237 <param name="imp_segment" value="6.0"/> | 244 <param name="imp_segment" value="6.0"/> |
267 .. class:: infomark | 274 .. class:: infomark |
268 | 275 |
269 **HapMap genetic maps** | 276 **HapMap genetic maps** |
270 | 277 |
271 HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available | 278 HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available |
272 in `this link <http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_ | 279 in `this links <https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_ |
273 | 280 |
274 ---- | 281 ---- |
275 | 282 |
276 .. class:: infomark | 283 .. class:: infomark |
277 | 284 |