comparison funannotate_annotate.xml @ 7:b6b5cd37f2a2 draft

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

6:582fd74dc2a1

#if $remove:
    --remove '${remove}'
#end if

--cpus \${GALAXY_SLOTS:-2}

&&

mv output/annotate_results/*.gbk out.gbk &&
mv output/annotate_results/*.annotations.txt out.annotations.txt &&

        <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt">
            <filter>outputs and 'new_names_passed' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <conditional name="input">
                <param name="input_type" value="gbk" />
                <param name="genbank" value="predict_augustus/Genus_species.gbk" />
            </conditional>
            <param name="database" value="2021-07-20-120000" />

                <assert_contents>
                    <has_text text="Passed Description" />
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="input">
                <param name="input_type" value="gff" />
                <param name="gff" value="predict_augustus/Genus_species.gff3" />
                <param name="fasta" value="genome.fa" />
                <param name="species" value="Genus species" />

7:b6b5cd37f2a2

#if $remove:
    --remove '${remove}'
#end if

--cpus \${GALAXY_SLOTS:-2}

&&

## funannotate sometimes leaves multiple *part.tbl and *part.sqn files
## https://github.com/nextgenusfs/funannotate/issues/777
find output/annotate_results 
-regex ".*part_[0-9]\+\.\(sqn\|tbl\)$"
-delete

&&

mv output/annotate_results/*.gbk out.gbk &&
mv output/annotate_results/*.annotations.txt out.annotations.txt &&

        <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt">
            <filter>outputs and 'new_names_passed' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="16">
            <conditional name="input">
                <param name="input_type" value="gbk" />
                <param name="genbank" value="predict_augustus/Genus_species.gbk" />
            </conditional>
            <param name="database" value="2021-07-20-120000" />

                <assert_contents>
                    <has_text text="Passed Description" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="16">
            <conditional name="input">
                <param name="input_type" value="gff" />
                <param name="gff" value="predict_augustus/Genus_species.gff3" />
                <param name="fasta" value="genome.fa" />
                <param name="species" value="Genus species" />