annotate plot_muon.xml @ 2:a22688df6ed1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ commit bcf2ec32c3d13b29da55e0e638da7ddd7162c436

<tool id="plot_muon" name="muon plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@COPY_MUDATA@
@CMD@
        ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
@CMD_read_inputs@

#if $method.method == "pl.embedding"
plot = mu.pl.embedding(
    mdata,
    basis='$method.basis',
    @CMD_params_embedding@
    return_fig=True
)
plot.savefig("plot.$plot_ext")

#else if $method.method == "pl.histogram"
plot = mu.pl.histogram(
    mdata,
    #if $method.key_variables.type == "var_names"
        #set $key_list = mdata.var_names
    #else if $method.key_variables.type == "obs"
        #set $key_list = mdata.obs.select_dtypes(exclude=['category']).columns
    #else if $method.key_variables.type == "custom"
        #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
    #end if
    keys=$key_list,
    #if $method.groupby
    groupby='$method.groupby',
    #end if
    save='plot.$plot_ext'
)
os.rename(os.path.join('figures', 'histogram_plot.$plot_ext'), 'plot.$plot_ext')

#else if $method.method == "pl.mofa"
plot = mu.pl.mofa(
    mdata,
    @CMD_params_embedding@
    return_fig=True
)
plot.savefig("plot.$plot_ext")

#else if $method.method == "pl.mofa_loadings"
plot = mu.pl.mofa_loadings(
    mdata,
    #if $method.factors
    factors='$method.factors',
    #end if
    include_lowest=$method.include_lowest,
    #if str($method.n_points)
    n_points=$method.n_points,
    #end if
    save='plot.$plot_ext'
)
os.rename(os.path.join('figures', 'mofa_loadings_plot.$plot_ext'), 'plot.$plot_ext')

#else if $method.method == "pl.umap"
plot = mu.pl.umap(
    mdata,
    @CMD_params_embedding@
    return_fig=True
)
plot.savefig("plot.$plot_ext")

#end if

]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="inputs_mudata"/>
        <conditional name="method">
            <param name="method" type="select" label="Method used for plotting">
                    <option value="pl.embedding">Scatter: Scatter plot along observations (.obs column), using 'muon.pl.embedding'</option>
                    <option value="pl.histogram">Histogram: Plot Histogram of Fragment lengths within specified region, using 'muon.pl.histogram'</option>
                    <option value="pl.mofa">Scatter: Scatter plot in MOFA factor coordinates, using 'muon.pl.mofa'</option>
                    <option value="pl.mofa_loadings">Ranking: Rank genes according to contributions to MOFA factors, using 'muon.pl.mofa_loadings'</option>
                    <option value="pl.umap">Scatter: UMAP scatter plot, using 'muon.pl.umap'</option>
            </param>
            <when value="pl.embedding">
                <param argument="basis" type="text" value="X_mofa" label="Name of the obsm basis to use" help="can also be a basis inside any modality, e.g. 'rna:X_pca'">
                    <expand macro="sanitize_query" />
                </param>
                <expand macro="params_embedding"/>
            </when>
            <when value="pl.histogram">
                <expand macro="param_keys"/>
                <param argument="groupby" type="text" optional="true" label="Column name(s) of .obs slot of the AnnData object according to which the plot is split">
                    <expand macro="sanitize_query" />
                </param>
            </when>
            <when value="pl.mofa">
                <expand macro="params_embedding"/>
            </when>
            <when value="pl.mofa_loadings">
                <param argument="factors" type="text" optional="true" label="Comma separated list of factors" help="For example, '1,2,3' means [1, 2, 3], first, second, third factors">
                    <expand macro="sanitize_query" />
                </param>
                <param argument="include_lowest" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to show the variables with both highest and lowest loadings"/>
                <param argument="n_points" type="integer" optional="true" label="Number of variables to plot for each factor"/>
            </when>
            <when value="pl.umap">
                <expand macro="params_embedding"/>
            </when>
        </conditional>
        <param name="plot_ext" type="select" label="Type of output plot">
            <option value="png" selected="true">PNG</option>
            <option value="svg">SVG</option>
            <option value="pdf">PDF</option>
        </param>
        <expand macro="inputs_common_advanced" />
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
            <filter>plot_ext == 'png'</filter>
        </data>
        <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
            <filter>plot_ext == 'pdf'</filter>
        </data>
        <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
            <filter>plot_ext == 'svg'</filter>
        </data>
        <data name="hidden_output" format="txt" label="Log file" hidden="true" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- test1: pl.embedding -->
            <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
            <param name="method" value="pl.embedding"/>
            <param name="basis" value="X_mofa"/>
            <param name="color" value="rna:leiden,atac:leiden"/>
            <param name="use_raw" value="False"/>
            <param name="plot_ext" value="pdf"/>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="mu.pl.embedding"/>
                    <has_text_matching expression="basis='X_mofa'"/>
                    <has_text_matching expression="color=\['rna:leiden', 'atac:leiden'\]"/>
                    <has_text_matching expression="use_raw=False"/>
                </assert_contents>
            </output>
            <output name="out_pdf" ftype="pdf" location="https://zenodo.org/records/12570984/files/pl.embedding.pdf" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test2 pl.histogram -->
            <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
            <param name="method" value="pl.histogram"/>
            <conditional name="key_variables">
                <param name="type" value="custom"/>
                <param name="keys" value="rna:n_genes_by_counts,rna:total_counts"/>
            </conditional>
            <param name="plot_ext" value="png"/>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="mu.pl.histogram"/>
                    <has_text_matching expression="keys=\['rna:n_genes_by_counts', 'rna:total_counts'\]"/>
                </assert_contents>
            </output>
            <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.histogram.png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test3: pl.mofa -->
            <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
            <param name="method" value="pl.mofa"/>
            <param name="use_raw" value="False"/>
            <param name="plot_ext" value="svg"/>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="mu.pl.mofa"/>
                    <has_text_matching expression="use_raw=False"/>
                </assert_contents>
            </output>
            <output name="out_svg" ftype="svg" location="https://zenodo.org/records/12570984/files/pl.mofa.svg" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test4: pl.mofa_loadings -->
            <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.mofa.h5mu"/>
            <param name="method" value="pl.mofa_loadings"/>
            <param name="factors" value="1,2,3"/>
            <param name="include_lowest" value="True"/>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="mu.pl.mofa_loadings"/>
                    <has_text_matching expression="factors='1,2,3'"/>
                    <has_text_matching expression="include_lowest=True"/>
                </assert_contents>
            </output>
            <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.mofa_loadings.png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test5: pl.umap -->
            <param name="mdata" location="https://zenodo.org/records/12570984/files/tl.umap.h5mu"/>
            <param name="method" value="pl.umap"/>
            <param name="use_raw" value="False"/>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="mu.pl.umap"/>
                    <has_text_matching expression="use_raw=False"/>
                </assert_contents>
            </output>
            <output name="out_png" ftype="png" location="https://zenodo.org/records/12570984/files/pl.umap.png" compare="image_diff"/>
        </test>
    </tests>
    <help><![CDATA[
Scatter: Scatter plot along observations (.obs column) ('muon.pl.embedding')
============================================================================

        Produce a scatter plot in the define basis (.obs), which can also be a basis inside any modality.

        More details on the `muon documentation
        <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.embedding.html#muon.pl.embedding>`__

Scatter: Scatter plot in MOFA factor coordinates ('muon.pl.mofa')
=================================================================

        Scatter plot in MOFA factors coordinates.

        More details on the `muon documentation
        <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.mofa.html#muon.pl.mofa>`__

Scatter: UMAP scatter plot ('muon.pl.umap')
===========================================

        UMAP Scatter plot.

        More details on the `muon documentation
        <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.umap.html#muon.pl.umap>`__

Histogram: Plot Histogram of Fragment lengths within specified region ('muon.pl.histogram')
===========================================================================================

        Plot Histogram of Fragment lengths within specified region.

        More details on the `muon documentation
        <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.histogram.html#muon.pl.histogram>`__

Ranking: Rank genes according to contributions to MOFA factors ('muon.pl.mofa_loadings')
========================================================================================

        Rank genes according to contributions to MOFA factors.

        More details on the `muon documentation
        <https://muon.readthedocs.io/en/latest/api/generated/muon.pl.mofa_loadings.html#muon.pl.mofa_loadings>`__
    ]]></help>
    <expand macro="citations"/>
</tool>