comparison seurat_dim_plot.xml @ 1:d539788175d4 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6

0:4f3a5ecefce5

<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>
    <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

        <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='Whether to label the 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="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)'/>
    </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**

    * PNG-format image file

.. _Seurat: https://www.nature.com/articles/nbt.4096
.. _Satija Lab: https://satijalab.org/seurat/


    ]]></help>
    <expand macro="citations" />
</tool>

1:d539788175d4

<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

        <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**

    * 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>