Mercurial > repos > iuc > snapatac2_plotting
diff plotting.xml @ 1:fecf9664c885 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
| author | iuc |
|---|---|
| date | Thu, 23 May 2024 15:19:43 +0000 |
| parents | 0cfd2d2f7351 |
| children | 05bd4db20227 |
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--- a/plotting.xml Thu May 16 13:15:05 2024 +0000 +++ b/plotting.xml Thu May 23 15:19:43 2024 +0000 @@ -8,20 +8,20 @@ <command detect_errors="exit_code"><![CDATA[ @PREP_ADATA@ @CMD@ - ]]></command> + ]]></command> <configfiles> <configfile name="script_file"><![CDATA[ @CMD_imports@ @CMD_read_inputs@ #if $method.method == 'pl.frag_size_distr' - #if $method.log_scale + #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 + #else sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) - #end if + #end if #else if $method.method == 'pl.tsse' sa.pl.tsse( adata, @@ -30,28 +30,32 @@ ) #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 = $method.sample_size, - @CMD_params_render_plot@ + adata, + color = '$method.color', + use_rep = '$method.use_rep', + #if $method.marker_size + marker_size = $method.marker_size, + #end if + marker_opacity = $method.marker_opacity, + #if $method.sample_size + sample_size = $method.sample_size, + #end if + @CMD_params_render_plot@ ) #else if $method.method == 'pl.regions' sa.pl.regions( - adata, - groupby = '$method.groupby', - peaks = '$method.peaks', - @CMD_params_render_plot@ + adata, + groupby = '$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@ + adata, + @CMD_params_render_plot@ ) #end if - ]]></configfile> + ]]></configfile> </configfiles> <inputs> <conditional name="method"> @@ -106,7 +110,7 @@ <!-- 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="adata" location="https://zenodo.org/records/11260316/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"/> @@ -114,7 +118,7 @@ <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="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="hidden_output"> <assert_contents> <has_text_matching expression="sa.pl.frag_size_distr"/> @@ -127,7 +131,7 @@ <!-- 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="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/> <param name="min_fragment" value="500"/> <param name="out_file" value="png"/> <expand macro="render_plot_test"/> @@ -142,13 +146,13 @@ <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"/> + <output name="out_png" location="https://zenodo.org/records/11260316/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="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/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"/> @@ -171,13 +175,13 @@ <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"/> + <output name="out_svg" location="https://zenodo.org/records/11260316/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"/> + <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="out_file" value="pdf"/> </conditional> @@ -190,7 +194,7 @@ <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"/> + <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help><![CDATA[