comparison funannotate_predict.xml @ 7:51b6ee65ef7f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2589d2785ca90160a22a5fe14e03311e189ea51d

6:7abc5f6dd595

                <has_text text="Running Augustus gene prediction using genus_species parameters"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test>

                <has_text text="Running Augustus gene prediction using fly parameters"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test>

                <has_text text="Training Augustus using BUSCO gene models"/>
                <has_text text="Aligning transcript evidence to genome with minimap2"/>
                <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
            </assert_stderr>
            <assert_command>
                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

                <has_text text="Training Augustus using BUSCO gene models"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
            </assert_stderr>
            <assert_command>
                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

7:51b6ee65ef7f

                <has_text text="Running Augustus gene prediction using genus_species parameters"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test>

                <has_text text="Running Augustus gene prediction using fly parameters"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test>

                <has_text text="Training Augustus using BUSCO gene models"/>
                <has_text text="Aligning transcript evidence to genome with minimap2"/>
                <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 21 preliminary alignments with diamond"/>
            </assert_stderr>
            <assert_command>
                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

                <has_text text="Training Augustus using BUSCO gene models"/>
                <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
                <has_text text="Found 21 preliminary alignments with diamond"/>
            </assert_stderr>
            <assert_command>
                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>