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comparison unicycler.xml @ 5:23300b42ca18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit fbcae3c133b8f34507da0d931212435f7772999f
author iuc
date Wed, 19 Sep 2018 17:07:02 -0400
parents 2db911a4efc5
children 0a3a602cd1e3
comparison
equal deleted inserted replaced
4:2db911a4efc5 5:23300b42ca18
175 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/> 175 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
176 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> 176 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
177 </section> 177 </section>
178 </inputs> 178 </inputs>
179 <outputs> 179 <outputs>
180 <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> 180 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
181 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> 181 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
182 </outputs> 182 </outputs>
183 <tests> 183 <tests>
184 <test> 184 <test>
185 <conditional name="paired_unpaired"> 185 <conditional name="paired_unpaired">
211 <param name="min_dead_end_size" value="1000"/> 211 <param name="min_dead_end_size" value="1000"/>
212 </section> 212 </section>
213 <section name="lr_align"> 213 <section name="lr_align">
214 <param name="scores" value="3,-6,-5,-2"/> 214 <param name="scores" value="3,-6,-5,-2"/>
215 </section> 215 </section>
216 <output name="assembly_graph" ftype="txt"> 216 <output name="assembly_graph" ftype="tabular">
217 <assert_contents> 217 <assert_contents>
218 <has_text text="TACGGGGAAGGACGTC"/> 218 <has_text text="TACGGGGAAGGACGTC"/>
219 </assert_contents> 219 </assert_contents>
220 </output> 220 </output>
221 <output name="assembly" ftype="fasta"> 221 <output name="assembly" ftype="fasta">
266 <param name="min_dead_end_size" value="1000"/> 266 <param name="min_dead_end_size" value="1000"/>
267 </section> 267 </section>
268 <section name="lr_align"> 268 <section name="lr_align">
269 <param name="scores" value="3,-6,-5,-2"/> 269 <param name="scores" value="3,-6,-5,-2"/>
270 </section> 270 </section>
271 <output name="assembly_graph" ftype="txt"> 271 <output name="assembly_graph" ftype="tabular">
272 <assert_contents> 272 <assert_contents>
273 <has_text text="TACGGGGAAGGACGTC" /> 273 <has_text text="TACGGGGAAGGACGTC" />
274 </assert_contents> 274 </assert_contents>
275 </output> 275 </output>
276 <output name="assembly" ftype="fasta"> 276 <output name="assembly" ftype="fasta">
313 <param name="min_dead_end_size" value="1000"/> 313 <param name="min_dead_end_size" value="1000"/>
314 </section> 314 </section>
315 <section name="lr_align"> 315 <section name="lr_align">
316 <param name="scores" value="3,-6,-5,-2"/> 316 <param name="scores" value="3,-6,-5,-2"/>
317 </section> 317 </section>
318 <output name="assembly_graph" ftype="txt"> 318 <output name="assembly_graph" ftype="tabular">
319 <assert_contents> 319 <assert_contents>
320 <has_text text="TACGGGGAAGGACGTC" /> 320 <has_text text="TACGGGGAAGGACGTC" />
321 </assert_contents> 321 </assert_contents>
322 </output> 322 </output>
323 <output name="assembly" ftype="fasta"> 323 <output name="assembly" ftype="fasta">
333 <param name="min_anchor_seg_len" value="10"/> 333 <param name="min_anchor_seg_len" value="10"/>
334 <section name="spades"> 334 <section name="spades">
335 <param name="kmers" value="21,23"/> 335 <param name="kmers" value="21,23"/>
336 </section> 336 </section>
337 <param name="long" value="only_long.fasta" ftype="fasta" /> 337 <param name="long" value="only_long.fasta" ftype="fasta" />
338 <output name="assembly_graph" ftype="txt"> 338 <output name="assembly_graph" ftype="tabular">
339 <assert_contents> 339 <assert_contents>
340 <has_text text="S" /> 340 <has_text text="S" />
341 </assert_contents> 341 </assert_contents>
342 </output> 342 </output>
343 <output name="assembly" ftype="fasta"> 343 <output name="assembly" ftype="fasta">