<macros>
    <xml name="factor_repeat">
        <repeat name="rep_factorName" title="Factor" min="1">
            <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
                help="Only letters, numbers and underscores will be retained in this field">
                <sanitizer>
                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
                </sanitizer>
            </param>
            <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
                    help="Only letters, numbers and underscores will be retained in this field">
                    <sanitizer>
                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
                    </sanitizer>
                </param>
                <yield/>
            </repeat>
        </repeat>
    </xml>
    <xml name="reference_target_levels">
        <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/>
        <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@DESEQ2_VERSION@">bioconductor-deseq2</requirement>
            <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
            <requirement type="package" version="2.44.0">bioconductor-rhdf5</requirement>
            <requirement type="package" version="1.28.0">bioconductor-tximport</requirement>
            <requirement type="package" version="1.52.1">bioconductor-genomicfeatures</requirement>
            <requirement type="package" version="1.20.3">r-getopt</requirement>
            <requirement type="package" version="0.9.3">r-ggrepel</requirement>
            <requirement type="package" version="3.1.3">r-gplots</requirement>
            <requirement type="package" version="1.0.12">r-pheatmap</requirement>
            <requirement type="package" version="0.2.21">r-rjson</requirement>
            <requirement type="package" version="0.1_3">r-base64enc</requirement>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">2.11.40.8</token>
    <token name="@DESEQ2_VERSION@">1.40.2</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_3308</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_3800</edam_operation>
        </edam_operations>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13059-014-0550-8</citation>
        </citations>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">DESeq2</xref>
            <xref type="bioconductor">deseq2</xref>
        </xrefs>
      </xml>
</macros>