New and updated Bioconductor tooling for single-cell analysis #7961
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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> | ||
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| <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> | ||
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| <token name="@CMD@"><![CDATA[ | ||
| cp '$input_loom' sce.loom && | ||
| cat '$script_file' > '$hidden_output' && | ||
| Rscript '$script_file' >> '$hidden_output' | ||
| ]]></token> | ||
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| <token name="@CMD_imports@"><![CDATA[ | ||
| library(scater) | ||
| library(LoomExperiment) | ||
| ]]></token> | ||
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| <token name="@CMD_read_inputs@"><![CDATA[ | ||
| sce <- import('sce.loom', format = "loom", type = "SingleCellLoomExperiment") | ||
| ]]></token> | ||
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| <xml name="input_sce"> | ||
| <param name="input_loom" type="data" format="loom" | ||
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Author
There was a problem hiding this comment. I initially took the RDS path, but had a discussion here encouraging me to use loom instead
Member
There was a problem hiding this comment. It's a great choice! Please make sure that the outputs are also always loom so that we don't need to use conversion tools in between. |
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| label="Input SingleCellExperiment (loom)"/> | ||
| </xml> | ||
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| <xml name="inputs_common_advanced"> | ||
| <section name="advanced_common" title="Advanced Output" expanded="false"> | ||
| <param name="show_log" type="boolean" checked="false" | ||
| label="Output log?"/> | ||
| </section> | ||
| </xml> | ||
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| <xml name="outputs_common_advanced"> | ||
| <data name="hidden_output" format="txt" | ||
| label="${tool.name} on ${on_string}: log"> | ||
| <filter>advanced_common['show_log']</filter> | ||
| </data> | ||
| </xml> | ||
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| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1093/bioinformatics/btw777</citation> | ||
| </citations> | ||
| </xml> | ||
| </macros> | ||
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| <?xml version="1.0"?> | ||
| <tool id="scater_plotcoldata" name="Scater: Plot column data" | ||
| version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>from a SingleCellExperiment object</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| @CMD@ | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="script_file"><![CDATA[ | ||
| @CMD_imports@ | ||
| @CMD_read_inputs@ | ||
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| p <- scater::plotColData( | ||
| object = sce, | ||
| y = '$y' | ||
| #if $x | ||
| , x = '$x' | ||
| #end if | ||
| ) | ||
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| 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"/> | ||
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Member
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| </assert_contents> | ||
| </output> | ||
| <output name="output_png" ftype="png"> | ||
| <assert_contents> | ||
| <has_size size="43418" delta="10"/> | ||
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Member
There was a problem hiding this comment. there are better asserts for images, such as |
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| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| **What it does** | ||
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| 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. | ||
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| **Inputs** | ||
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| - 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``). | ||
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| **Outputs** | ||
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| - A PNG image of the plot. | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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| categories: | ||
| - Transcriptomics | ||
| - Single-cell | ||
| description: Galaxy wrappers for the Bioconductor scuttle package (v1.20.0) | ||
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| long_description: | | ||
| scuttle provides utility functions for single-cell RNA-seq analysis, | ||
| including quality control, normalisation, and transformation, built | ||
| around the SingleCellExperiment class. | ||
| name: scuttle | ||
| owner: iuc | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| <?xml version="1.0"?> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">1.20.0</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">23.0</token> | ||
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| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">bioconductor-scuttle</requirement> | ||
| <requirement type="package" version="1.28.0">bioconductor-loomexperiment</requirement> | ||
| <yield/> | ||
| </requirements> | ||
| </xml> | ||
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| <!-- Mirrors @CMD@ in seurat/macros.xml --> | ||
| <token name="@CMD@"><![CDATA[ | ||
| cp '$input_loom' sce.loom && | ||
| cat '$script_file' > '$hidden_output' && | ||
| Rscript '$script_file' >> '$hidden_output' | ||
| ]]></token> | ||
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| <!-- Mirrors @CMD_imports@ in seurat/macros.xml --> | ||
| <token name="@CMD_imports@"><![CDATA[ | ||
| library(scuttle) | ||
| library(LoomExperiment) | ||
| ]]></token> | ||
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| <!-- Mirrors @CMD_read_inputs@ in seurat/macros.xml --> | ||
| <token name="@CMD_read_inputs@"><![CDATA[ | ||
| sce <- import('sce.loom', format = "loom", type = "SingleCellLoomExperiment") | ||
| ]]></token> | ||
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| <!-- Mirrors @CMD_loom_write_outputs@ in seurat/macros.xml --> | ||
| <token name="@CMD_loom_write_outputs@"><![CDATA[ | ||
| export(sce, "output.loom", format = "loom") | ||
| ]]></token> | ||
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| <xml name="input_sce"> | ||
| <param name="input_loom" type="data" format="loom" | ||
| label="Input SingleCellExperiment (loom)"/> | ||
| </xml> | ||
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| <xml name="output_sce"> | ||
| <data name="output_loom" format="loom" from_work_dir="output.loom" | ||
| label="${tool.name} on ${on_string}: loom"/> | ||
| <expand macro="outputs_common_advanced"/> | ||
| </xml> | ||
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| <xml name="inputs_common_advanced"> | ||
| <section name="advanced_common" title="Advanced Output" expanded="false"> | ||
| <param name="show_log" type="boolean" checked="false" | ||
| label="Output log?"/> | ||
| </section> | ||
| </xml> | ||
|
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| <xml name="outputs_common_advanced"> | ||
| <data name="hidden_output" format="txt" | ||
| label="${tool.name} on ${on_string}: log"> | ||
| <filter>advanced_common['show_log']</filter> | ||
| </data> | ||
| </xml> | ||
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| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1093/bioinformatics/btw777</citation> | ||
| </citations> | ||
| </xml> | ||
| </macros> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| <?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@ | ||
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| subsets <- list() | ||
| #for $s in $subsets_repeat | ||
| subsets[['${s.name}']] <- which(rownames(sce) %in% readLines('$s.feature_file')) | ||
| #end for | ||
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| sce <- scuttle::addPerCellQCMetrics( | ||
| x = sce, | ||
| subsets = subsets, | ||
| assay.type = '$assay_type' | ||
| ) | ||
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| @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** | ||
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| Runs ``scuttle::addPerCellQCMetrics()`` on a ``SingleCellExperiment`` object | ||
| and returns the same object with new columns appended to ``colData``: | ||
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| - ``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) | ||
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| **Inputs** | ||
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| - 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). | ||
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| **Outputs** | ||
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| - The same ``SingleCellExperiment`` with QC columns added to ``colData``, | ||
| saved as a loom file. | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> |
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importa scater function? or bioconductor function?There was a problem hiding this comment.
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import()is a generic defined inBiocIOwith methods defined in other packages likertracklayer.The
SingleCellLoomExperimenttype is defined in the packageLoomExperimenthere https://github.com/Bioconductor/LoomExperiment/blob/devel/R/import-method.R#L135I haven't studied the internals of the
import()function, but from the choice of three types it sounds like this helps theimport()function work with the different "flavours" of Bioconductor single-cell objects that can be stored in loom files