| Next changeset 1:daeca8f7a26e (2019-11-25) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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README seurat_dim_plot.xml seurat_macros.xml |
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| diff -r 000000000000 -r 6e26ee99fdfc README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Apr 03 11:20:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +Seurat tools |
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| diff -r 000000000000 -r 6e26ee99fdfc seurat_dim_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_dim_plot.xml Wed Apr 03 11:20:03 2019 -0400 |
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| @@ -0,0 +1,115 @@ +<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0"> + <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description> + <macros> + <import>seurat_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"><![CDATA[ + seurat-dim-plot.R + --input-object-file '$input' + #if $reduction_use + --reduction-use '$reduction_use' + #end if + #if $dim_1 + --dim-1 $dim_1 + #end if + #if $dim_2 + --dim-2 $dim_2 + #end if + #if $cells_use + --cells-use $cells_use + #end if + #if $pt_size + --pt-size $pt_size + #end if + #if $label_size + --label-size $label_size + #end if + --do-label $do_label + #if $group_by + --group-by $group_by + #end if + #if $plot_title + --plot-title '$plot_title' + #end if + --do-bare $do_bare + #if $cols_use + --cols-use '$cols_use' + #end if + #if $pt_shape + --pt-shape '$pt_shape' + #end if + --coord-fixed $coord_fixed + --no-axes $no_axes + --dark-theme $dark_theme + #if $plot_order + --plot-order '$plot_order' + #end if + --png-width $png_width + --png-height $png_height + --output-image-file $output_image_file + ]]></command> + <inputs> + <param type="data" name="input" format="rdata" label="RDS object" help='File in which a serialized R matrix object may be found'/> + <param type="text" name="reduction_use" value='pca' label="Dimensionality reduction" help='Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed' /> + <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' /> + <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' /> + <param type="data" name="cells_use" format="tabular" label="Cells list" help='File to be used to derive a vector of cells to plot (default is all cells)' optional='true'/> + <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' /> + <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/> + <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" /> + <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' /> + <param type="text" name="plot_title" format="text" label='Plot title' /> + <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" /> + <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' /> + <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" help='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' /> + <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" /> + <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" /> + <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" /> + <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' /> + <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' /> + <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/> + </inputs> + <outputs> + <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input" value="seurat_clustered.rds" /> + <output name="output_image_file" file="pca.png" /> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing +data. It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to +identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to +integrate diverse types of single cell data. + +This tool graphs the output of a dimensional reduction technique (PCA by default). Cells are colored +by their identity class. + +----- + +**Inputs** + + * Seurat RDS object + +----- + +**Outputs** + + * PNG-format image file + +.. _Seurat: https://www.nature.com/articles/nbt.4096 +.. _Satija Lab: https://satijalab.org/seurat/ + +@VERSION_HISTORY@ + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 6e26ee99fdfc seurat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_macros.xml Wed Apr 03 11:20:03 2019 -0400 |
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| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<macros> + + <token name="@VERSION@">0.0.5</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">seurat-scripts</requirement> + </requirements> + </xml> + + <xml name="version"> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + + <xml name="genes-use-input"> + <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> + </xml> + <xml name="dims-use-input"> + <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/> + </xml> + + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. + +2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l). + ]]></token> + + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.4096</citation> + <citation type="bibtex"> + @misc{r-seurat-scripts.git, + author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team}, + year = {2018}, + title = {Seurat-scripts: command line interface for Seurat}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, + } + </citation> + </citations> + </xml> +</macros> |