Mercurial > repos > iuc > stacks2_ustacks

comparison stacks_ustacks.xml @ 1:aa646fe5a0b4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:00:37 -0400
parents 9eaeea3fb1bb
children 1dce9f3949c9
comparison
equal deleted inserted replaced
0:9eaeea3fb1bb 1:aa646fe5a0b4
147 </test> 147 </test>
148 <!-- manual selected list of elements + non-default short args, test for file presence --> 148 <!-- manual selected list of elements + non-default short args, test for file presence -->
149 <test> 149 <test>
150 <param name="input_type|input_type_select" value="single"/> 150 <param name="input_type|input_type_select" value="single"/>
151 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 151 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
152 <param name="-m" value="2" /> 152 <param name="m" value="2" />
153 <param name="-M" value="3" /> 153 <param name="M" value="3" />
154 <param name="-N" value="4"/> 154 <param name="N" value="4"/>
155 <param name="-R" value="-R" /> 155 <param name="R" value="-R" />
156 <param name="-H" value="-H" /> 156 <param name="H" value="-H" />
157 <param name="add_log" value="yes" /> 157 <param name="add_log" value="yes" />
158 <assert_command> 158 <assert_command>
159 <has_text text="-m 2" /> 159 <has_text text="-m 2" />
160 <has_text text="-M 3" /> 160 <has_text text="-M 3" />
161 <has_text text="-N 5" /> 161 <has_text text="-N 4" />
162 <has_text text="-R" /> 162 <has_text text="-R" />
163 <has_text text="-H" /> 163 <has_text text="-H" />
164 </assert_command> 164 </assert_command>
165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
166 <output_collection name="tabs" count="6"> 166 <output_collection name="tabs" count="6">
199 <param name="bc_err_freq" value="0.1"/> 199 <param name="bc_err_freq" value="0.1"/>
200 </conditional> 200 </conditional>
201 <param name="gapped|use_gapped" value="no" /> 201 <param name="gapped|use_gapped" value="no" />
202 <param name="add_log" value="yes" /> 202 <param name="add_log" value="yes" />
203 <assert_command> 203 <assert_command>
204 <has_text text="--model_type bounded" /> 204 <has_text text="--model_type snp" />
205 <has_text text="--alpha 0.1" /> 205 <has_text text="--alpha 0.1" />
206 <has_text text="--bound_low 0.1" /> 206 <not_has_text text="--bound_low 0.1" />
207 <has_text text="--bound_high 0.5" /> 207 <not_has_text text="--bound_high 0.5" />
208 <has_text text="--bc_err_freq 0.1" /> 208 <not_has_text text="--bc_err_freq 0.1" />
209 <has_text text="--disable-gapped" /> 209 <has_text text="--disable-gapped" />
210 </assert_command> 210 </assert_command>
211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
212 <output_collection name="tabs" count="6"> 212 <output_collection name="tabs" count="6">
213 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 213 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
225 <collection type="list"> 225 <collection type="list">
226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
227 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> 227 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
228 </collection> 228 </collection>
229 </param> 229 </param>
230 <param name="assembly_options|keep_high_cov" value="--keep-high-cov"/> 230 <param name="assembly_options|keep_high_cov" value="true"/>
231 <param name="assembly_options|d" value="-d" /> 231 <param name="assembly_options|d" value="-d" />
232 <param name="assembly_options|high_cov_thres" value="2.0"/> 232 <param name="assembly_options|high_cov_thres" value="2.0"/>
233 <param name="assembly_options|max_locus_stacks" value="4" /> 233 <param name="assembly_options|max_locus_stacks" value="4" />
234 <param name="assembly_options|k_len" value="12"/> 234 <param name="assembly_options|k_len" value="12"/>
235 <param name="gapped|use_gapped" value="yes" /> 235 <param name="gapped|use_gapped" value="yes" />
241 <has_text text="-d" /> 241 <has_text text="-d" />
242 <has_text text="--high_cov_thres 2.0" /> 242 <has_text text="--high_cov_thres 2.0" />
243 <has_text text="--max_locus_stacks 4" /> 243 <has_text text="--max_locus_stacks 4" />
244 <has_text text="--k_len 12" /> 244 <has_text text="--k_len 12" />
245 <has_text text="--max_gaps 3" /> 245 <has_text text="--max_gaps 3" />
246 <has_text text="--min_aln_len 3" /> 246 <has_text text="--min_aln_len 0.7" />
247 </assert_command> 247 </assert_command>
248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
249 <output_collection name="tabs" count="6"> 249 <output_collection name="tabs" count="6">
250 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 250 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
251 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 251 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>