Mercurial > repos > iuc > snapatac2_plotting
diff plotting.xml @ 0:0cfd2d2f7351 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
| author | iuc |
|---|---|
| date | Thu, 16 May 2024 13:15:05 +0000 |
| parents | |
| children | fecf9664c885 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotting.xml Thu May 16 13:15:05 2024 +0000 @@ -0,0 +1,229 @@ +<tool id="snapatac2_plotting" name="SnapATAC2 Plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="requirements"/> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +@PREP_ADATA@ +@CMD@ + ]]></command> + <configfiles> + <configfile name="script_file"><![CDATA[ +@CMD_imports@ +@CMD_read_inputs@ + +#if $method.method == 'pl.frag_size_distr' + #if $method.log_scale +fig = sa.pl.frag_size_distr(adata, show=False) +fig.update_yaxes(type="log") +sa.pl.render_plot(fig, @CMD_params_render_plot@) + #else +sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) + #end if +#else if $method.method == 'pl.tsse' +sa.pl.tsse( + adata, + min_fragment = $method.min_fragment, + @CMD_params_render_plot@ +) +#else if $method.method == 'pl.umap' +sa.pl.umap( + adata, + color = '$method.color', + use_rep = '$method.use_rep', + marker_size = $method.marker_size, + marker_opacity = $method.marker_opacity, + sample_size = $method.sample_size, + @CMD_params_render_plot@ +) +#else if $method.method == 'pl.regions' +sa.pl.regions( + adata, + groupby = '$method.groupby', + peaks = '$method.peaks', + @CMD_params_render_plot@ +) +#else if $method.method == 'pl.spectral_eigenvalues' +sa.pl.spectral_eigenvalues( + adata, + @CMD_params_render_plot@ +) +#end if + ]]></configfile> + </configfiles> + <inputs> + <conditional name="method"> + <param name="method" type="select" label="Method used for plotting"> + <option value="pl.frag_size_distr">Plot fragment size distribution, using 'pl.frag_size_distr'</option> + <option value="pl.tsse">Plot the TSS enrichment vs. number of fragments density figure, using 'pl.tsse'</option> + <option value="pl.umap">Plot the UMAP embedding, using 'pl.umap'</option> + <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option> + </param> + <when value="pl.frag_size_distr"> + <expand macro="inputs_anndata"/> + <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/> + <expand macro="params_render_plot"/> + </when> + <when value="pl.tsse"> + <expand macro="inputs_anndata"/> + <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/> + <expand macro="params_render_plot"/> + </when> + <when value="pl.umap"> + <expand macro="inputs_anndata"/> + <param argument="color" type="text" value="" optional="true" label="Color"/> + <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/> + <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/> + <param argument="marker_opacity" type="float" value="1" label="Opactiy of the dots"/> + <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/> + <expand macro="params_render_plot"/> + </when> + <when value="pl.spectral_eigenvalues"> + <expand macro="inputs_anndata"/> + <expand macro="params_render_plot"/> + </when> + </conditional> + <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>method['out_file'] == '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>method['out_file'] == '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>method['out_file'] == '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"> + <!-- pl.frag_size_distr --> + <conditional name="method"> + <param name="method" value="pl.frag_size_distr"/> + <param name="adata" location="https://zenodo.org/records/11199963/files/pp.import_data.pbmc_500_chr21.h5ad"/> + <param name="log_scale" value="True"/> + <param name="out_file" value="pdf"/> + <expand macro="render_plot_test"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true"/> + </section> + <output name="out_pdf" location="https://zenodo.org/records/11199963/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sa.pl.frag_size_distr"/> + <has_text_matching expression="fig.update_yaxes"/> + <expand macro="render_plot_matching_text"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <!-- pl.tsse --> + <conditional name="method"> + <param name="method" value="pl.tsse"/> + <param name="adata" location="https://zenodo.org/records/11199963/files/metrics.tsse.pbmc_500_chr21.h5ad"/> + <param name="min_fragment" value="500"/> + <param name="out_file" value="png"/> + <expand macro="render_plot_test"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true"/> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sa.pl.tsse"/> + <has_text_matching expression="min_fragment = 500"/> + <expand macro="render_plot_matching_text"/> + </assert_contents> + </output> + <output name="out_png" location="https://zenodo.org/records/11199963/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + </test> + <test expect_num_outputs="2"> + <!-- pl.umap --> + <conditional name="method"> + <param name="method" value="pl.umap"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.leiden.pbmc_500_chr21.h5ad"/> + <param name="color" value="leiden"/> + <param name="use_rep" value="X_umap"/> + <param name="marker_size" value="1"/> + <param name="marker_opacity" value="0.8"/> + <param name="sample_size" value="100"/> + <expand macro="render_plot_test"/> + <param name="out_file" value="svg"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true"/> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sa.pl.umap"/> + <has_text_matching expression="color = 'leiden'"/> + <has_text_matching expression="use_rep = 'X_umap'"/> + <has_text_matching expression="marker_size = 1"/> + <has_text_matching expression="marker_opacity = 0.8"/> + <has_text_matching expression="sample_size = 100"/> + <expand macro="render_plot_matching_text"/> + </assert_contents> + </output> + <output name="out_svg" location="https://zenodo.org/records/11199963/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> + </test> + <test expect_num_outputs="2"> + <!-- pl.spectral_eigenvalues --> + <conditional name="method"> + <param name="method" value="pl.spectral_eigenvalues"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/> + <expand macro="render_plot_test"/> + <param name="out_file" value="pdf"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true"/> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sa.pl.spectral_eigenvalues"/> + <expand macro="render_plot_matching_text"/> + </assert_contents> + </output> + <output name="out_pdf" location="https://zenodo.org/records/11199963/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + </test> + </tests> + <help><![CDATA[ +Plot fragment size distribution, using `pl.frag_size_distr` +=========================================================== + +Plot fragment size distribution. + +`metrics.frag_size_distr` must be ran first in order to use this function. + +Plot the TSS enrichment vs. number of fragments density figure, using `pl.tsse` +=============================================================================== + +Plot the TSS enrichment vs. number of fragments density figure. + +More details on the `SnapATAC2 documentation +<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__ + +Plot the UMAP embedding, using `pl.umap` +======================================== + +Plot the UMAP embedding. + +More details on the `SnapATAC2 documentation +<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ + +Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues` +=========================================================================== + +Plot the eigenvalues of spectral embedding. + +More details on the `SnapATAC2 documentation +<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ + ]]></help> + <expand macro="citations"/> +</tool>