comparison nextclade.xml @ 18:feb40665d7cd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb

17:07ab9bd68a02

        #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,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>

            <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" name="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" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
                <param argument="--input-tree" name="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" name="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" name="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" name="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" name="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>

            </conditional>
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="MPXV" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="66" />
                    <has_text text="hMPXV-1" />
                </assert_contents>
            </output>
        </test>
    </tests>

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>

            <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>

            </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>