Mercurial > repos > iuc > coverm_contig

comparison coverm_contig.xml @ 2:f8cb3f0a19fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 877d09f04bae57678daa94766fd31d0d0f1b6a37
author iuc
date Tue, 28 Mar 2023 08:36:07 +0000
parents 688a777e1b19
children c2a5823e4763
comparison
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1:688a777e1b19 2:f8cb3f0a19fa
270 </element> 270 </element>
271 </collection> 271 </collection>
272 </param> 272 </param>
273 <param name="ref_fasta_history" value="7seqs.fna"/> 273 <param name="ref_fasta_history" value="7seqs.fna"/>
274 </conditional> 274 </conditional>
275 <output name="output1" file="contig_test1.tsv" ftype="tsv"/> 275 <output name="output1" file="contig_test1.tsv" ftype="tsv" sort="true"/>
276 </test> 276 </test>
277 <test> 277 <test>
278 <conditional name="reads"> 278 <conditional name="reads">
279 <param name="read_type" value="single"/> 279 <param name="read_type" value="single"/>
280 <param name="single" value="bad_reads.interleaved.fq"/> 280 <param name="single" value="bad_reads.interleaved.fq"/>
284 <param name="contig_end_exclusion" value="0"/> 284 <param name="contig_end_exclusion" value="0"/>
285 </section> 285 </section>
286 <section name="out"> 286 <section name="out">
287 <param name="output_format" value="sparse"/> 287 <param name="output_format" value="sparse"/>
288 </section> 288 </section>
289 <output name="output1" file="contig_test2.tsv" ftype="tsv"/> 289 <output name="output1" file="contig_test2.tsv" ftype="tsv" sort="true"/>
290 </test> 290 </test>
291 <test> 291 <test>
292 <conditional name="reads"> 292 <conditional name="reads">
293 <param name="read_type" value="interleaved"/> 293 <param name="read_type" value="interleaved"/>
294 <param name="single" value="bad_reads.all.interleaved.fa"/> 294 <param name="single" value="bad_reads.all.interleaved.fa"/>
302 <param name="proper_pairs_only" value="true"/> 302 <param name="proper_pairs_only" value="true"/>
303 </section> 303 </section>
304 <section name="out"> 304 <section name="out">
305 <param name="output_format" value="sparse"/> 305 <param name="output_format" value="sparse"/>
306 </section> 306 </section>
307 <output name="output1" file="contig_test3.tsv" ftype="tsv"/> 307 <output name="output1" file="contig_test3.tsv" ftype="tsv" sort="true"/>
308 </test> 308 </test>
309 <test> 309 <test>
310 <conditional name="reads"> 310 <conditional name="reads">
311 <param name="read_type" value="paired"/> 311 <param name="read_type" value="paired"/>
312 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/> 312 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/>
332 <param name="contig_end_exclusion" value="0"/> 332 <param name="contig_end_exclusion" value="0"/>
333 </section> 333 </section>
334 <section name="mapping"> 334 <section name="mapping">
335 <param name="--min-read-percent-identity" value="0.95"/> 335 <param name="--min-read-percent-identity" value="0.95"/>
336 </section> 336 </section>
337 <output name="output1" file="contig_test4.tsv" ftype="tsv"/> 337 <output name="output1" file="contig_test4.tsv" ftype="tsv" sort="true"/>
338 </test> 338 </test>
339 <test> 339 <test>
340 <conditional name="reads"> 340 <conditional name="reads">
341 <param name="read_type" value="bam"/> 341 <param name="read_type" value="bam"/>
342 <param name="bam" value="tpm_test.bam"/> 342 <param name="bam" value="tpm_test.bam"/>
346 <param name="tpm" value="true"/> 346 <param name="tpm" value="true"/>
347 </section> 347 </section>
348 <section name="out"> 348 <section name="out">
349 <param name="output_format" value="sparse"/> 349 <param name="output_format" value="sparse"/>
350 </section> 350 </section>
351 <output name="output1" file="contig_test5.tsv" ftype="tsv"/> 351 <output name="output1" file="contig_test5.tsv" ftype="tsv" sort="true"/>
352 </test> 352 </test>
353 </tests> 353 </tests>
354 <help><![CDATA[ 354 <help><![CDATA[
355 .. class:: infomark 355 .. class:: infomark
356 356