Mercurial > repos > iuc > funannotate_predict

comparison funannotate_predict.xml @ 2:33092577d65d draft

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"planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
author iuc
date Thu, 21 Oct 2021 07:32:20 +0000
parents 1a59958c1f76
children 73909ee8162e
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1:1a59958c1f76 2:33092577d65d
62 #end if 62 #end if
63 #if $est_list: 63 #if $est_list:
64 --transcript_evidence $est_list 64 --transcript_evidence $est_list
65 #end if 65 #end if
66 66
67 #if $evidences.prot_evidence == 'custom': 67 #if $evidences.prot_evidence.prot_evidence_source == 'custom':
68 --protein_evidence 68 --protein_evidence
69 #for $protev in $evidences.protein_evidence: 69 #for $protev in $evidences.prot_evidence.protein_evidence:
70 '${protev}' 70 '${protev}'
71 #end for 71 #end for
72 #end if 72 #end if
73 --p2g_pident ${evidences.p2g_pident} 73 --p2g_pident ${evidences.p2g_pident}
74 --p2g_prefilter ${evidences.p2g_prefilter} 74 --p2g_prefilter ${evidences.p2g_prefilter}
504 <has_text text="Running Augustus gene prediction using genus_species parameters"/> 504 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
505 <has_text text="Training Augustus using BUSCO gene models"/> 505 <has_text text="Training Augustus using BUSCO gene models"/>
506 <has_text text="Aligning transcript evidence to genome with minimap2"/> 506 <has_text text="Aligning transcript evidence to genome with minimap2"/>
507 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> 507 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
508 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> 508 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
509 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/> 509 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
510 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/> 510 <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
511 </assert_stderr> 511 </assert_stderr>
512 <assert_command>
513 <has_text text="--protein_evidence"/>
514 </assert_command>
512 </test> 515 </test>
513 516
514 <!-- proteins --> 517 <!-- proteins -->
515 <test> 518 <test>
516 <param name="input" value="genome_masked.fa" /> 519 <param name="input" value="genome_masked.fa" />
575 <has_text text="Running Augustus gene prediction using genus_species parameters"/> 578 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
576 <has_text text="Training Augustus using BUSCO gene models"/> 579 <has_text text="Training Augustus using BUSCO gene models"/>
577 <not_has_text text="Aligning transcript evidence to genome with minimap2"/> 580 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
578 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> 581 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
579 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> 582 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
580 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/> 583 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
581 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/> 584 <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
582 </assert_stderr> 585 </assert_stderr>
586 <assert_command>
587 <has_text text="--protein_evidence"/>
588 </assert_command>
583 </test> 589 </test>
584 </tests> 590 </tests>
585 <help><![CDATA[ 591 <help><![CDATA[
586 Funannotate_ predict 592 Funannotate_ predict
587 -------------------- 593 --------------------