Mercurial > repos > iuc > snapatac2_plotting
diff plotting.xml @ 6:1ac4a5f05f33 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
| author | iuc |
|---|---|
| date | Tue, 25 Nov 2025 16:41:12 +0000 |
| parents | 05bd4db20227 |
| children |
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--- a/plotting.xml Thu Nov 07 13:07:52 2024 +0000 +++ b/plotting.xml Tue Nov 25 16:41:12 2025 +0000 @@ -7,30 +7,31 @@ <expand macro="requirements"/> </requirements> <command detect_errors="exit_code"><![CDATA[ -@PREP_ADATA@ +@CMD_PREP_ADATA@ @CMD@ ]]></command> <configfiles> <configfile name="script_file"><![CDATA[ -@CMD_imports@ -@CMD_read_inputs@ +@CONF_IMPORTS@ +@CONF_READ_INPUTS@ #if $method.method == 'pl.frag_size_distr' #if $method.log_scale -fig = sa.pl.frag_size_distr(adata, show=False) +fig = snap.pl.frag_size_distr(adata, show=False) fig.update_yaxes(type="log") -sa.pl.render_plot(fig, @CMD_params_render_plot@) +snap.pl.render_plot(fig, @CONF_PARAMS_RENDER_PLOT@) #else -sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) +snap.pl.frag_size_distr(adata, @CONF_PARAMS_RENDER_PLOT@) #end if + #else if $method.method == 'pl.tsse' -sa.pl.tsse( +snap.pl.tsse( adata, min_fragment = $method.min_fragment, - @CMD_params_render_plot@ + @CONF_PARAMS_RENDER_PLOT@ ) #else if $method.method == 'pl.umap' -sa.pl.umap( +snap.pl.umap( adata, color = '$method.color', use_rep = '$method.use_rep', @@ -41,19 +42,13 @@ #if $method.sample_size sample_size = $method.sample_size, #end if - @CMD_params_render_plot@ + @CONF_PARAMS_RENDER_PLOT@ ) -#else if $method.method == 'pl.regions' -sa.pl.regions( + +#else if $method.method == 'pl.spectral_eigenvalues' +snap.pl.spectral_eigenvalues( adata, - groupby = '$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@ + @CONF_PARAMS_RENDER_PLOT@ ) #end if ]]></configfile> @@ -67,30 +62,31 @@ <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"/> + <expand macro="param_inputs_anndata"/> + <param argument="use_rep" type="text" value="frag_size_distr" label="Use the indicated representation in .obsm"/> <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.tsse"> - <expand macro="inputs_anndata"/> + <expand macro="param_inputs_anndata"/> <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.umap"> - <expand macro="inputs_anndata"/> - <param argument="color" type="text" value="" optional="true" label="Color"/> + <expand macro="param_inputs_anndata"/> + <param argument="color" type="text" value="" optional="true" label="Color" help="Color to use for the points. retrieved from .obs"/> <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="marker_opacity" type="float" value="1" label="Opacity of the dots"/> <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.spectral_eigenvalues"> - <expand macro="inputs_anndata"/> - <expand macro="params_render_plot"/> + <expand macro="param_inputs_anndata"/> + <expand macro="param_render_plot"/> </when> </conditional> - <expand macro="inputs_common_advanced"/> + <expand macro="param_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}"> @@ -102,6 +98,9 @@ <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="out_html" format="html" from_work_dir="plot.html" label="HTML plot from ${tool.name} (${method.method}) on ${on_string}"> + <filter>method['out_file'] == 'html'</filter> + </data> <data name="hidden_output" format="txt" label="Log file" hidden="true"> <filter>advanced_common['show_log']</filter> </data> @@ -111,20 +110,20 @@ <!-- pl.frag_size_distr --> <conditional name="method"> <param name="method" value="pl.frag_size_distr"/> - <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/> + <param name="adata" location="https://zenodo.org/records/17512085/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"/> + <expand macro="test_param_render_plot"/> </conditional> <section name="advanced_common"> <param name="show_log" value="true"/> </section> - <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + <output name="out_pdf" location="https://zenodo.org/records/17512085/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="snap.pl.frag_size_distr"/> <has_text_matching expression="fig.update_yaxes"/> - <expand macro="render_plot_matching_text"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> </test> @@ -132,34 +131,41 @@ <!-- pl.tsse --> <conditional name="method"> <param name="method" value="pl.tsse"/> - <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/> + <param name="adata" location="https://zenodo.org/records/17512085/files/metrics.tsse.pbmc_500_chr21.h5ad"/> <param name="min_fragment" value="500"/> <param name="out_file" value="png"/> - <expand macro="render_plot_test"/> + <expand macro="test_param_render_plot"/> </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="snap.pl.tsse"/> <has_text_matching expression="min_fragment = 500"/> - <expand macro="render_plot_matching_text"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + <output name="out_png"> + <assert_contents> + <has_image_center_of_mass center_of_mass="325,223" eps="30"/> + <has_image_channels channels="4"/> + <has_image_height height="450"/> + <has_image_width width="650"/> + </assert_contents> + </output> </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/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.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"/> + <expand macro="test_param_render_plot"/> <param name="out_file" value="svg"/> </conditional> <section name="advanced_common"> @@ -167,23 +173,23 @@ </section> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.umap"/> + <has_text_matching expression="snap.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"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> + <output name="out_svg" location="https://zenodo.org/records/17512085/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/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/> - <expand macro="render_plot_test"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/> + <expand macro="test_param_render_plot"/> <param name="out_file" value="pdf"/> </conditional> <section name="advanced_common"> @@ -191,11 +197,11 @@ </section> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.spectral_eigenvalues"/> - <expand macro="render_plot_matching_text"/> + <has_text_matching expression="snap.pl.spectral_eigenvalues"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + <output name="out_pdf" location="https://zenodo.org/records/17512085/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help><![CDATA[ @@ -212,7 +218,7 @@ 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>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__ Plot the UMAP embedding, using `pl.umap` ======================================== @@ -220,7 +226,7 @@ Plot the UMAP embedding. More details on the `SnapATAC2 documentation -<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues` =========================================================================== @@ -228,7 +234,7 @@ Plot the eigenvalues of spectral embedding. More details on the `SnapATAC2 documentation -<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ ]]></help> <expand macro="citations"/> </tool>