comparison nextclade.xml @ 2:6cd62b6d2b5c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"

1:0f20ed06ed6c

<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@">0.14.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        nextclade
        --input-fasta '${input_fasta}'
        #if $outputs and "report_tsv" in $outputs
            --output-tsv report.tsv
        #end if 
        #if $outputs and "report_json" in $outputs
            --output-json '${report_json}'
        #end if 
        #if $outputs and "output_tree" in $outputs

            #end if 
            #if $adv.input_pcr_primers
                --input-pcr-primers '${adv.input_pcr_primers}'
            #end if
        #end if
        #if $outputs and "report_tsv" in $outputs
        && tail -n-1 report.tsv >'$report_tsv'
        #end if 
    ]]></command>
    <inputs>
        <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
        <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
            <option value="report_json">JSON format report</option>
            <option value="report_tsv" selected="true">Tabular format report</option>
            <option value="output_tree">Auspice v2 tree file (JSON format)</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>

2:6cd62b6d2b5c

<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@">0.14.3</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        nextclade
        --input-fasta '${input_fasta}'
        #if $outputs and "report_tsv" in $outputs
            #if $include_header
                --output-tsv '$report_tsv'
            #else
                --output-tsv report.tsv
            #end if
        #end if 
        #if $outputs and "report_json" in $outputs
            --output-json '${report_json}'
        #end if 
        #if $outputs and "output_tree" in $outputs

            #end if 
            #if $adv.input_pcr_primers
                --input-pcr-primers '${adv.input_pcr_primers}'
            #end if
        #end if
        #if $outputs and "report_tsv" in $outputs and not $include_header
            && tail -n+2 report.tsv >'$report_tsv'
        #end if 
    ]]></command>
    <inputs>
        <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
        <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
            <option value="report_json">JSON format report</option>
            <option value="report_tsv" selected="true">Tabular format report</option>
            <option value="output_tree">Auspice v2 tree file (JSON 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>