tools-iuc/tools/scuttle-1.20.0/scuttle_addpercellqcmetrics.xml at 09f01a0c44e764c09a68dd6cf1e36a80b0a3aa79 · galaxyproject/tools-iuc · GitHub

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<?xml version="1.0"?>
<tool id="scuttle_addpercellqcmetrics" name="Scuttle: Add per-cell QC metrics"
      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to 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@

subsets <- list()
#for $s in $subsets_repeat
subsets[['${s.name}']] <- which(rownames(sce) %in% readLines('$s.feature_file'))
#end for

sce <- scuttle::addPerCellQCMetrics(
    x          = sce,
    subsets    = subsets,
    assay.type = '$assay_type'
)

@CMD_loom_write_outputs@
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="input_sce"/>
        <param name="assay_type" type="text" value="counts"
               label="Assay to use for QC computation"/>
        <repeat name="subsets_repeat" title="Gene subset" min="0">
            <param name="name" type="text" label="Subset name"
                   help="Short label, e.g. MT"/>
            <param name="feature_file" type="data" format="txt"
                   label="Feature list"
                   help="Plain text file with one rowname per line, no header"/>
        </repeat>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <expand macro="output_sce"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- test1: no subsets -->
            <param name="input_loom" location="https://zenodo.org/records/19665848/files/sce_with_mitochondrial_features.loom" ftype="loom"/>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="addPerCellQCMetrics"/>
                </assert_contents>
            </output>
            <output name="output_loom" ftype="loom">
                <assert_contents>
                    <has_size size="34822" delta="10"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- test2: MT subset -->
            <param name="input_loom" location="https://zenodo.org/records/19665848/files/sce_with_mitochondrial_features.loom" ftype="loom"/>
            <repeat name="subsets_repeat">
                <param name="name" value="MT"/>
                <param name="feature_file" value="mitochondrial_gene_ids.txt" ftype="txt"/>
            </repeat>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="addPerCellQCMetrics"/>
                </assert_contents>
            </output>
            <output name="output_loom" ftype="loom">
                <assert_contents>
                    <has_size size="45032" delta="10"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Runs ``scuttle::addPerCellQCMetrics()`` on a ``SingleCellExperiment`` object
and returns the same object with new columns appended to ``colData``:

- ``sum`` – total counts per cell
- ``detected`` – number of detected features per cell
- ``subsets_<name>_sum``, ``subsets_<name>_detected``, ``subsets_<name>_percent``
  for each user-defined gene subset (e.g. mitochondrial genes)

**Inputs**

- A ``SingleCellExperiment`` object saved as a loom file.
- Optionally, one or more named gene subsets, each defined by a plain text file
  listing the rownames to include (one per line, no header).

**Outputs**

- The same ``SingleCellExperiment`` with QC columns added to ``colData``,
  saved as a loom file.
    ]]></help>
    <expand macro="citations"/>
</tool>