comparison nextclade.xml @ 5:0c46b95d60c3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"

4:b74b9a7b3e3b

<tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
        <token name="@TOOL_VERSION@">1.2.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
        <requirement type="package">coreutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" &&
        ln -s "\$DB_PATH" db &&
        #set $input_qc_config = "db/qc.json"
        #set $input_root_seq = "db/reference.fasta"
        #set $input_tree = "db/tree.json"
        #set $input_gene_map = "db/genemap.gff"
        #set $input_pcr_primers = "db/primers.csv"

            <option value="report_tsv" selected="true">Tabular format report</option>
            <option value="output_tree">Auspice v2 tree file (JSON format)</option>
            <option value="output_fasta">Aligned sequences (FASTA format)</option>
        </param>
        <param name="include_header" type="boolean" label="Include header line in output file" 
            truevalue="true" falsevalue="false" />        
        <conditional name="adv">
            <param name="advanced_options" type="select" label="Use advanced options" >
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="48" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv,report_json,output_tree" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="48" />
                    <has_text text="20A" />
                </assert_contents>

            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <conditional name="adv">
                <param name="advanced_options" value="yes" />
                <param name="input_qc_config" value="strict_qc.json" ftype="json" />
            </conditional>
            <output name="report_tsv">

5:0c46b95d60c3

<tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
        <requirement type="package">coreutils</requirement>
    </requirements>
    <version_command>nextclade --version-detailed</version_command>
    <command detect_errors="exit_code"><![CDATA[
        nextclade dataset get -n '${organism}' -o db &&
        #set $input_qc_config = "db/qc.json"
        #set $input_root_seq = "db/reference.fasta"
        #set $input_tree = "db/tree.json"
        #set $input_gene_map = "db/genemap.gff"
        #set $input_pcr_primers = "db/primers.csv"

            <option value="report_tsv" selected="true">Tabular format report</option>
            <option value="output_tree">Auspice v2 tree file (JSON format)</option>
            <option value="output_fasta">Aligned sequences (FASTA format)</option>
        </param>
        <param name="include_header" type="boolean" label="Include header line in output file" 
            truevalue="true" falsevalue="false" />
        <param name="organism" type="select" label="Organism">
            <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
            <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
            <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
            <option value="flu_vic_ha">Influenza B Victoria HA</option>
            <option value="flu_yam_ha">Influenza B Yamagata HA</option>
        </param>   
        <conditional name="adv">
            <param name="advanced_options" type="select" label="Use advanced options" >
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="sars-cov-2" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="48" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv,report_json,output_tree" />
            <param name="organism" value="sars-cov-2" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="48" />
                    <has_text text="20A" />
                </assert_contents>

            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="sars-cov-2" />
            <conditional name="adv">
                <param name="advanced_options" value="yes" />
                <param name="input_qc_config" value="strict_qc.json" ftype="json" />
            </conditional>
            <output name="report_tsv">