Mercurial > repos > iuc > coverm_genome

comparison coverm_genome.xml @ 2:5bf5792b0996 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 08:36:25 +0000
parents a671907f96fe
children bb3f59096c8e
comparison
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1:a671907f96fe 2:5bf5792b0996
441 <param name="variance" value="true"/> 441 <param name="variance" value="true"/>
442 </section> 442 </section>
443 <section name="out"> 443 <section name="out">
444 <param name="output_format" value="sparse"/> 444 <param name="output_format" value="sparse"/>
445 </section> 445 </section>
446 <output name="output1" file="test1.tsv" ftype="tsv"/> 446 <output name="output1" file="test1.tsv" ftype="tsv" sort="true"/>
447 </test> 447 </test>
448 <test expect_num_outputs="1"> 448 <test expect_num_outputs="1">
449 <conditional name="reads"> 449 <conditional name="reads">
450 <param name="read_type" value="bam"/> 450 <param name="read_type" value="bam"/>
451 <param name="bam" value="7seqs.reads_for_seq1_and_seq2.bam"/> 451 <param name="bam" value="7seqs.reads_for_seq1_and_seq2.bam"/>
467 <param name="relative_abundance" value="true"/> 467 <param name="relative_abundance" value="true"/>
468 </section> 468 </section>
469 <section name="out"> 469 <section name="out">
470 <param name="output_format" value="sparse"/> 470 <param name="output_format" value="sparse"/>
471 </section> 471 </section>
472 <output name="output1" file="test2.tsv" ftype="tsv"/> 472 <output name="output1" file="test2.tsv" ftype="tsv" sort="true"/>
473 </test> 473 </test>
474 <test expect_num_outputs="1"> 474 <test expect_num_outputs="1">
475 <section name="derep"> 475 <section name="derep">
476 <param name="dereplicate" value="true"/> 476 <param name="dereplicate" value="true"/>
477 <param name="genome_info" value="genomeInfo.csv"/> 477 <param name="genome_info" value="genomeInfo.csv"/>
526 </section> 526 </section>
527 <section name="out"> 527 <section name="out">
528 <param name="dereplication_output_cluster_definition" value="true"/> 528 <param name="dereplication_output_cluster_definition" value="true"/>
529 <param name="dereplication_output_representative_fasta_directory_copy" value="true"/> 529 <param name="dereplication_output_representative_fasta_directory_copy" value="true"/>
530 </section> 530 </section>
531 <output name="output1" file="test3.tsv" ftype="tsv"/> 531 <output name="output1" file="test3.tsv" ftype="tsv" sort="true"/>
532 <output name="cluster_definition" ftype="tsv" value="test4_cluster.tsv"/> 532 <output name="cluster_definition" ftype="tsv" value="test4_cluster.tsv" sort="true"/>
533 <output_collection name="representative_fasta" type="list" count="3"> 533 <output_collection name="representative_fasta" type="list" count="3">
534 <element name="genome1" file="test4_rep1.fa" ftype="fasta" /> 534 <element name="genome1" file="test4_rep1.fa" ftype="fasta" />
535 <element name="genome2" file="test4_rep2.fa" ftype="fasta" /> 535 <element name="genome2" file="test4_rep2.fa" ftype="fasta" />
536 <element name="genome3" file="test4_rep3.fa" ftype="fasta" /> 536 <element name="genome3" file="test4_rep3.fa" ftype="fasta" />
537 </output_collection> 537 </output_collection>
547 </conditional> 547 </conditional>
548 <section name="cov"> 548 <section name="cov">
549 <param name="count" value="true"/> 549 <param name="count" value="true"/>
550 <param name="min_covered_fraction" value="0"/> 550 <param name="min_covered_fraction" value="0"/>
551 </section> 551 </section>
552 <output name="output1" file="test5.tsv" ftype="tsv"/> 552 <output name="output1" file="test5.tsv" ftype="tsv" sort="true"/>
553 </test> 553 </test>
554 </tests> 554 </tests>
555 <help><![CDATA[ 555 <help><![CDATA[
556 .. class:: infomark 556 .. class:: infomark
557 557