Mercurial > repos > iuc > coverm_contig

comparison coverm_contig.xml @ 4:92a66ccb7e6c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
author iuc
date Fri, 18 Aug 2023 09:22:33 +0000
parents cc7863bec4e0
children
comparison
equal deleted inserted replaced
3:cc7863bec4e0 4:92a66ccb7e6c
229 </test> 229 </test>
230 <test expect_num_outputs="1"> 230 <test expect_num_outputs="1">
231 <conditional name="mapped"> 231 <conditional name="mapped">
232 <param name="mapped" value="not-mapped" /> 232 <param name="mapped" value="not-mapped" />
233 <conditional name="mode"> 233 <conditional name="mode">
234 <param name="mode" value="individual"/>
235 <conditional name="read_type">
236 <param name="type" value="paired_collection"/>
237 <param name="paired_reads">
238 <collection type="paired">
239 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
240 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
241 </collection>
242 </param>
243 </conditional>
244 <param name="reference" value="7seqs.fna" />
245 <param name="sharded" value="" />
246 </conditional>
247 </conditional>
248 <section name="alignment">
249 <param name="min_read_aligned_length" value="0" />
250 <param name="min_read_percent_identity" value="0" />
251 <param name="min_read_aligned_percent" value="0" />
252 <conditional name="proper_pairs_only">
253 <param name="proper_pairs_only" value=""/>
254 </conditional>
255 <param name="exclude_supplementary" value=""/>
256 </section>
257 <section name="cov">
258 <param name="methods" value="mean"/>
259 <param name="trim_min" value="5"/>
260 <param name="trim_max" value="95"/>
261 <param name="min_covered_fraction" value="10"/>
262 <param name="contig_end_exclusion" value="75"/>
263 </section>
264 <param name="output_format" value="dense"/>
265 <output name="output" ftype="tabular">
266 <assert_contents>
267 <has_text text="Contig"/>
268 <has_text text="Mean"/>
269 <has_text text="7seqs.fna"/>
270 <has_text text="genome1~random_sequence_length_11000"/>
271 <has_text text="genome2~seq1"/>
272 </assert_contents>
273 </output>
274 </test>
275 <test expect_num_outputs="1">
276 <conditional name="mapped">
277 <param name="mapped" value="not-mapped" />
278 <conditional name="mode">
234 <param name="mode" value="co"/> 279 <param name="mode" value="co"/>
235 <conditional name="read_type"> 280 <conditional name="read_type">
236 <param name="type" value="single"/> 281 <param name="type" value="single"/>
237 <param name="single" value="bad_reads.interleaved.fq"/> 282 <param name="single" value="bad_reads.interleaved.fq"/>
238 </conditional> 283 </conditional>