comparison nextclade.xml @ 1:0f20ed06ed6c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"

0:615f484bdb4a

<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@">0</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
    ]]></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>

            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
            <filter>outputs and "report_tsv" in outputs</filter>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>
        <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">

        <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_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_text text="20A" />
                </assert_contents>
            </output>
            <output name="report_json">
                <assert_contents>

                <param name="advanced_options" value="yes" />
                <param name="input_qc_config" value="strict_qc.json" ftype="json" />
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
        </test>
    </tests>

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>

            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
            <filter>outputs and "report_tsv" in outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertionsmissing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss
                ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit
                es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus
                teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" />
            </actions>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>
        <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">

        <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="41" />
                    <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="41" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
            <output name="report_json">
                <assert_contents>

                <param name="advanced_options" value="yes" />
                <param name="input_qc_config" value="strict_qc.json" ftype="json" />
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="41" />
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
        </test>
    </tests>