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comparison beagle.xml @ 1:d0a6954d0a0a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
author iuc
date Sun, 22 Jan 2023 12:42:30 +0000
parents 117d42db0a30
children ab97b3b44590
comparison
equal deleted inserted replaced
0:117d42db0a30 1:d0a6954d0a0a
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