Mercurial > repos > ebi-gxa > seurat_dim_plot
diff seurat_dim_plot.xml @ 1:d539788175d4 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
| author | ebi-gxa |
|---|---|
| date | Wed, 13 Mar 2019 12:53:31 -0400 |
| parents | 4f3a5ecefce5 |
| children | 4e73c73291cd |
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--- a/seurat_dim_plot.xml Mon Mar 04 12:18:09 2019 -0500 +++ b/seurat_dim_plot.xml Wed Mar 13 12:53:31 2019 -0400 @@ -1,13 +1,13 @@ -<tool id="seurat_dim_plot" name="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> +<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 '$input' + seurat-dim-plot.R + --input-object-file '$input' #if $reduction_use --reduction-use '$reduction_use' #end if @@ -58,18 +58,18 @@ <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='Whether to label the clusters' truevalue="TRUE" falsevalue="FALSE" /> + <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='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='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='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='Setting to TRUE will remove the axes.' 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='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='Width of png (px)' /> - <param type="integer" name="png_height" value='1000' label='Height of png (px)'/> + <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}"/> @@ -77,8 +77,8 @@ <tests> <test> <param name="input" value="seurat_clustered.rds" /> - <output name="output_image_file" file="pca.png" /> - </test> + <output name="output_image_file" file="pca.png" /> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -108,6 +108,7 @@ .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ +@VERSION_HISTORY@ ]]></help> <expand macro="citations" />