Mercurial > repos > iuc > plot_muon
diff plot_muon.xml @ 0:36f2cd69d20e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ commit bcf2ec32c3d13b29da55e0e638da7ddd7162c436
| author | iuc |
|---|---|
| date | Wed, 05 Feb 2025 10:53:37 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_muon.xml Wed Feb 05 10:53:37 2025 +0000 @@ -0,0 +1,271 @@ +<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> \ No newline at end of file