comparison nextclade.xml @ 19:128ba8da994f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8

18:feb40665d7cd

        #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" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" />
        <param name="organism" type="select" label="Organism">
            <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
            <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</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>
            <option value="MPXV">Monkeypox (All Clades)</option>
            <option value="hMPXV">Human Monkeypox (hMPXV)</option>
            <option value="hMPXV_B1">Human Monkeypox Clade B.1</option>
        </param>   
        <conditional name="db">
            <param name="source" type="select" label="Version of database to use">
                <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option>
                <option value="download">Download latest available database version from web</option>
            </param>
            <when value="cached">
                <param name="release" label="Cached nextclade database release" type="select">
                    <options from_data_table="nextclade">
                        <column name="value" index="0" />
                        <column name="description" index="2" />
                        <column name="date" index="4" />
                        <column name="path" index="5" />
                        <filter type="sort_by" column="4" />
                        <filter type="param_value" ref="organism" column="1" />
                        <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@" />
                    </options>
                </param>
            </when>
            <when value="download"></when>
        </conditional>
        <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>
            <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>
            <when value="yes">
                <param argument="--input-qc-config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" />
                <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
                <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
                <param argument="--input-gene-map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" />
                <param argument="--input-pcr-primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" />
                <param argument="--input-virus-properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." />
                <param argument="--include-reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" />                
            </when>
            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
            <filter>outputs and "report_tsv" in outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="seqName,clade,Nextclade_pango,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,isReverseComplement,failedGenes,warnings,errors" />
            </actions>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>

            <filter>outputs and "output_fasta" in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="sars-cov-2" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="66" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <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="66" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
            <output name="report_json">
                <assert_contents>
                    <has_text text='"pos": 240,' />
                </assert_contents>
            </output>
            <output name="output_tree">
                <assert_contents>
                    <has_text text='"title": "QC Status"' />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <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">
                <assert_contents>
                    <has_n_columns n="66" />
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <param name="outputs" value="report_tsv,output_fasta" />
            <param name="organism" value="sars-cov-2" />
            <conditional name="adv">
                <param name="advanced_options" value="yes" />
                <param name="include_reference" value="true" />
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="66" />
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
            <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" />
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="MPXV" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="67" />
                    <has_text text="hMPXV-1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

* An Auspice v2 tree file in JSON format

.. _Nextclade: https://github.com/nextstrain/nextclade

    ]]></help>
    <expand macro="citations" />
</tool>

19:128ba8da994f

        #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" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences"/>
        <param name="organism" type="select" label="Organism">
            <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
            <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
            <option value="sars-cov-2-21L">SARS-CoV-2 relative to BA.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>
            <option value="MPXV">Monkeypox (All Clades - MPXV)</option>
            <option value="hMPXV">Human Monkeypox (hMPXV)</option>
            <option value="hMPXV_B1">Human Monkeypox Clade B.1 (hMPXV_B1)</option>
        </param>
        <conditional name="db">
            <param name="source" type="select" label="Version of database to use">
                <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option>
                <option value="download">Download latest available database version from web</option>
            </param>
            <when value="cached">
                <param name="release" label="Cached nextclade database release" type="select">
                    <options from_data_table="nextclade">
                        <column name="value" index="0"/>
                        <column name="description" index="2"/>
                        <column name="date" index="4"/>
                        <column name="path" index="5"/>
                        <filter type="sort_by" column="4"/>
                        <filter type="param_value" ref="organism" column="1"/>
                        <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@"/>
                    </options>
                </param>
            </when>
            <when value="download"/>
        </conditional>
        <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>
            <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>
            <when value="yes">
                <param argument="--input-qc-config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration"/>
                <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence"/>
                <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree"/>
                <param argument="--input-gene-map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes"/>
                <param argument="--input-pcr-primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites"/>
                <param argument="--input-virus-properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation."/>
                <param argument="--include-reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file"/>
            </when>
            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
            <filter>outputs and "report_tsv" in outputs</filter>
            <actions>
                <conditional name="organism">
                    <expand macro="column_metadata" dataset_name="sars-cov-2" extra_columns="Nextclade_pango,"/>
                    <expand macro="column_metadata" dataset_name="sars-cov-2-no-recomb" extra_columns="Nextclade_pango,"/>
                    <expand macro="column_metadata" dataset_name="sars-cov-2-21L" extra_columns="Nextclade_pango,partiallyAliased,immune_escape,ace2_binding,"/>
                    <expand macro="column_metadata" dataset_name="flu_h1n1pdm_ha"/>
                    <expand macro="column_metadata" dataset_name="flu_h3n2_ha"/>
                    <expand macro="column_metadata" dataset_name="flu_vic_ha"/>
                    <expand macro="column_metadata" dataset_name="flu_yam_ha"/>
                    <expand macro="column_metadata" dataset_name="MPXV" extra_columns="outbreak,lineage,"/>
                    <expand macro="column_metadata" dataset_name="hMPXV" extra_columns="outbreak,lineage,"/>
                    <expand macro="column_metadata" dataset_name="hMPXV_B1" extra_columns="outbreak,lineage,"/>
                </conditional>
            </actions>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>

            <filter>outputs and "output_fasta" in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
            <conditional name="db">
                <param name="source" value="download"/>
            </conditional>
            <param name="outputs" value="report_tsv"/>
            <param name="organism" value="sars-cov-2"/>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="67"/>
                    <has_text text="20A"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
            <conditional name="db">
                <param name="source" value="download"/>
            </conditional>
            <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="67"/>
                    <has_text text="20A"/>
                </assert_contents>
                <metadata name="column_names" value="seqName,clade,Nextclade_pango,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,coverage,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,isReverseComplement,failedGenes,warnings,errors"/>
            </output>
            <output name="report_json">
                <assert_contents>
                    <has_text text="&quot;pos&quot;: 240,"/>
                </assert_contents>
            </output>
            <output name="output_tree">
                <assert_contents>
                    <has_text text="&quot;title&quot;: &quot;QC Status&quot;"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
            <conditional name="db">
                <param name="source" value="download"/>
            </conditional>
            <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">
                <assert_contents>
                    <has_n_columns n="67"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
            <conditional name="db">
                <param name="source" value="download"/>
            </conditional>
            <param name="outputs" value="report_tsv,output_fasta"/>
            <param name="organism" value="sars-cov-2"/>
            <conditional name="adv">
                <param name="advanced_options" value="yes"/>
                <param name="include_reference" value="true"/>
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="67"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
            <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz"/>
            <conditional name="db">
                <param name="source" value="download"/>
            </conditional>
            <param name="outputs" value="report_tsv"/>
            <param name="organism" value="MPXV"/>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="68"/>
                    <has_text text="hMPXV-1"/>
                </assert_contents>
                <metadata name="column_names" value="seqName,clade,outbreak,lineage,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,coverage,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,isReverseComplement,failedGenes,warnings,errors"/>
            </output>
        </test>
    </tests>
    <help><![CDATA[

* An Auspice v2 tree file in JSON format

.. _Nextclade: https://github.com/nextstrain/nextclade

    ]]></help>
    <expand macro="citations"/>
</tool>