tools-iuc/tools/scater-1.38.0/macros.xml at 2281acbef3662bba0516139a1e3fdba94bd228dd · galaxyproject/tools-iuc · GitHub

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<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.38.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bioconductor-scater</requirement>
            <requirement type="package" version="1.28.0">bioconductor-loomexperiment</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@CMD@"><![CDATA[
cp '$input_loom' sce.loom &&
cat '$script_file' > '$hidden_output' &&
Rscript '$script_file' >> '$hidden_output'
    ]]></token>

    <token name="@CMD_imports@"><![CDATA[
library(scater)
library(LoomExperiment)
    ]]></token>

    <token name="@CMD_read_inputs@"><![CDATA[
sce <- import('sce.loom', format = "loom", type = "SingleCellLoomExperiment")
    ]]></token>

    <xml name="input_sce">
        <param name="input_loom" type="data" format="loom"
               label="Input SingleCellExperiment (loom)"/>
    </xml>

    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Output" expanded="false">
            <param name="show_log" type="boolean" checked="false"
                   label="Output log?"/>
        </section>
    </xml>

    <xml name="outputs_common_advanced">
        <data name="hidden_output" format="txt"
              label="${tool.name} on ${on_string}: log">
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btw777</citation>
        </citations>
    </xml>
</macros>