tools-iuc/tools/scater-1.38.0/scater_plotcoldata.xml at 09f01a0c44e764c09a68dd6cf1e36a80b0a3aa79 · galaxyproject/tools-iuc · GitHub

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<?xml version="1.0"?>
<tool id="scater_plotcoldata" name="Scater: Plot column data"
      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from a SingleCellExperiment object</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
@CMD_read_inputs@

p <- scater::plotColData(
    object = sce,
    y      = '$y'
#if $x
    , x = '$x'
#end if
)

ggplot2::ggsave('output.png', plot = p)
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="input_sce"/>
        <param name="y" type="text"
               label="Y-axis column"
               help="Column from colData to display on the y-axis (e.g. detected)"/>
        <param name="x" type="text" optional="true"
               label="X-axis column (optional)"
               help="Column from colData to display on the x-axis (e.g. sum). Leave empty for a violin/beeswarm plot."/>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <data name="output_png" format="png" from_work_dir="output.png"
              label="${tool.name} on ${on_string}: plot"/>
        <expand macro="outputs_common_advanced"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- test1: y only -->
            <param name="input_loom" location="https://zenodo.org/records/19665848/files/sce_after_addpercellqcmetrics.loom" ftype="loom"/>
            <param name="y" value="detected"/>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="plotColData"/>
                </assert_contents>
            </output>
            <output name="output_png" ftype="png">
                <assert_contents>
                    <has_size size="82793" delta="10"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- test2: y and x -->
            <param name="input_loom" location="https://zenodo.org/records/19665848/files/sce_after_addpercellqcmetrics.loom" ftype="loom"/>
            <param name="y" value="detected"/>
            <param name="x" value="sum"/>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="plotColData"/>
                </assert_contents>
            </output>
            <output name="output_png" ftype="png">
                <assert_contents>
                    <has_size size="43418" delta="10"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Runs ``scater::plotColData()`` on a ``SingleCellExperiment`` object to visualise
column-level metadata. Without an x-axis variable, each column is shown as a
violin/beeswarm plot. With an x-axis variable, a scatter plot is produced.

**Inputs**

- A ``SingleCellExperiment`` object saved as a loom file.
- The name of a ``colData`` column to display on the y-axis (e.g. ``detected``).
- Optionally, the name of a ``colData`` column to display on the x-axis (e.g. ``sum``).

**Outputs**

- A PNG image of the plot.
    ]]></help>
    <expand macro="citations"/>
</tool>