comparison funannotate_predict.xml @ 9:d6c7106b7b2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67

8:f31125bb85ea

            (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
        <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
    </outputs>
    <tests>
        <!-- training from scratch -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="busco">
                <param name="busco_seed_species" value="fly" />
                <param name="busco_db" value="insecta" />

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

        <!-- proteins -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

9:d6c7106b7b2e

            (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
        <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
    </outputs>
    <tests>
        <!-- training from scratch -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="busco">
                <param name="busco_seed_species" value="fly" />
                <param name="busco_db" value="insecta" />

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

        <!-- proteins -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>