comparison pangolin.xml @ 5:e2497d4385e2 draft default tip

"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 9e569ed56e07b5d2d3fb8a72ddc477d34570f081"

4:35566aadcfc7

        <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"

        </test>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <section name="additional">
                <param name="write_tree" value="true" />
            </section>
            <output name="lineage_report" >
                <assert_contents>
                    <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
                    <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />

5:e2497d4385e2

        <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 $additional.include_putative &&

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="include_putative" type="boolean" checked="false" argument="-p"
                truevalue="-p"
                falsevalue=""
                label="Include putative lineages"
                help="Putative lineages fit the criteria required for lineage designation but have not got recall values suitable for lineage assignment.
                If left as 'No', only lineages with >95% recall rate will be used."
            />
            <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"

        </test>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <section name="additional">
                <param name="write_tree" value="true" />
                <param name="include_putative" value="true" />
            </section>
            <output name="lineage_report" >
                <assert_contents>
                    <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
                    <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />