comparison pangolin.xml @ 1:b91b3923656e draft

"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 216d09e3d63a6ab4245df78c111ca97d4e0b14de"

0:f612c8391bd8

<tool id="pangolon" name="Pangolin" version="@VERSION@+galaxy0">
    <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
    <macros>
        <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'

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta"
            label="Input multi-sequence fasta file"
            />

                argument="--min-length"
                />
        </section>
    </inputs>
    <outputs>
        <data format="csv" from_work_dir="lineage_report.csv" 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.csv" />
        </test>
    </tests>
    <help><![CDATA[
    
Pangolin

1:b91b3923656e

<tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0">
    <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
    <macros>
        <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"
            label="Input multi-sequence fasta file"
            />

                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