comparison pangolin.xml @ 2:c897e502c084 draft

"planemo upload for repository https://github.com/hCoV-2019/pangolin commit b53db6d0612f94e5c9365c9ecd267eeff396097f"

1:b91b3923656e

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' &&

sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta"

                />
            <param name="min_length" type="integer" value="10000" min="0"
                label="Minimum query length to attempt assignment"
                argument="--min-length"
                />
        </section>
    </inputs>
    <outputs>
        <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <output name="lineage_report" value="lineage_report.tsv" />
        </test>
    </tests>
    <help><![CDATA[
    
Pangolin

2:c897e502c084

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' $additional.write_tree &&

sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta"

                />
            <param name="min_length" type="integer" value="10000" min="0"
                label="Minimum query length to attempt assignment"
                argument="--min-length"
                />
            <param name="write_tree" type="boolean" checked="false"
                truevalue="--write-tree"
                falsevalue=""
                label="Write guide trees"
                help="Output a collection of trees with each query sequence placed in the guide tree"
                />
        </section>
    </inputs>
    <outputs>
        <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
        <collection name="pangolin_trees" type="list" label="${tool.name} Trees">
            <filter>additional['write_tree']</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" directory="pangolin_trees/" format="iqtree" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <output name="lineage_report" value="lineage_report.tsv" />
        </test>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <section name="additional">
                <param name="write_tree" value="true" />
            </section>
            <output name="lineage_report" value="lineage_report.tsv" />
            <output_collection name="pangolin_trees" type="list">
                <element name="USA_NY-NYUMC7_2020_EPI_ISL_418192__USA_New_York_Manhattan_2020-03-16" ftype="iqtree">
                    <assert_contents>
                        <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
                    </assert_contents>
                </element>
                <element name="Japan_DP0779_2020_EPI_ISL_416626__Japan_unknown__2020-02-17" ftype="iqtree">
                    <assert_contents>
                        <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
    
Pangolin