Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 17:413ffec60330 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
author iuc
date Fri, 18 Oct 2024 10:33:42 +0000
parents ff6da5117343
children 6a2f9865e303
comparison
equal deleted inserted replaced
16:ff6da5117343 17:413ffec60330
221 221
222 #else if str($method.method) == 'pl.pca': 222 #else if str($method.method) == 'pl.pca':
223 sc.pl.pca( 223 sc.pl.pca(
224 @CMD_PARAM_PLOT_INPUTS@ 224 @CMD_PARAM_PLOT_INPUTS@
225 @CMD_PARAM_COLOR@ 225 @CMD_PARAM_COLOR@
226 @CMD_PARAM_GENE_SYMBOLS@
226 use_raw=$method.use_raw, 227 use_raw=$method.use_raw,
227 sort_order=$method.sort_order, 228 sort_order=$method.sort_order,
228 @CMD_PARAM_GROUPS@ 229 @CMD_PARAM_GROUPS@
229 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@ 230 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
230 @CMD_SCATTER_OUTINE@ 231 @CMD_SCATTER_OUTINE@
280 281
281 #else if str($method.method) == 'pl.umap': 282 #else if str($method.method) == 'pl.umap':
282 sc.pl.umap( 283 sc.pl.umap(
283 @CMD_PARAM_PLOT_INPUTS@ 284 @CMD_PARAM_PLOT_INPUTS@
284 @CMD_PARAM_COLOR@ 285 @CMD_PARAM_COLOR@
286 @CMD_PARAM_GENE_SYMBOLS@
285 use_raw=$method.use_raw, 287 use_raw=$method.use_raw,
286 @CMD_PL_EDGES@ 288 @CMD_PL_EDGES@
287 arrows=$method.arrows, 289 arrows=$method.arrows,
288 sort_order=$method.sort_order, 290 sort_order=$method.sort_order,
289 @CMD_PARAM_GROUPS@ 291 @CMD_PARAM_GROUPS@
295 297
296 #else if str($method.method) == 'pl.diffmap': 298 #else if str($method.method) == 'pl.diffmap':
297 sc.pl.diffmap( 299 sc.pl.diffmap(
298 @CMD_PARAM_PLOT_INPUTS@ 300 @CMD_PARAM_PLOT_INPUTS@
299 @CMD_PARAM_COLOR@ 301 @CMD_PARAM_COLOR@
302 @CMD_PARAM_GENE_SYMBOLS@
300 use_raw=$method.use_raw, 303 use_raw=$method.use_raw,
301 sort_order=$method.sort_order, 304 sort_order=$method.sort_order,
302 @CMD_PARAM_GROUPS@ 305 @CMD_PARAM_GROUPS@
303 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@ 306 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
304 @CMD_SCATTER_OUTINE@ 307 @CMD_SCATTER_OUTINE@
739 </param> 742 </param>
740 <expand macro="pl_figsize"/> 743 <expand macro="pl_figsize"/>
741 </when> 744 </when>
742 <when value="pl.pca"> 745 <when value="pl.pca">
743 <expand macro="param_color"/> 746 <expand macro="param_color"/>
747 <expand macro="param_gene_symbols"/>
744 <expand macro="param_use_raw"/> 748 <expand macro="param_use_raw"/>
745 <expand macro="param_sort_order"/> 749 <expand macro="param_sort_order"/>
746 <expand macro="param_groups"/> 750 <expand macro="param_groups"/>
747 <expand macro="params_pl_attribute_section"/> 751 <expand macro="params_pl_attribute_section"/>
748 <expand macro="params_scatter_outine"/> 752 <expand macro="params_scatter_outine"/>
782 <expand macro="section_matplotlib_pyplot_scatter"/> 786 <expand macro="section_matplotlib_pyplot_scatter"/>
783 <expand macro="param_layer"/> 787 <expand macro="param_layer"/>
784 </when> 788 </when>
785 <when value="pl.umap"> 789 <when value="pl.umap">
786 <expand macro="param_color"/> 790 <expand macro="param_color"/>
791 <expand macro="param_gene_symbols"/>
787 <expand macro="param_use_raw"/> 792 <expand macro="param_use_raw"/>
788 <expand macro="pl_edges"/> 793 <expand macro="pl_edges"/>
789 <expand macro="param_arrows"/> 794 <expand macro="param_arrows"/>
790 <expand macro="param_sort_order"/> 795 <expand macro="param_sort_order"/>
791 <expand macro="param_groups"/> 796 <expand macro="param_groups"/>
794 <expand macro="section_matplotlib_pyplot_scatter"/> 799 <expand macro="section_matplotlib_pyplot_scatter"/>
795 <expand macro="param_layer"/> 800 <expand macro="param_layer"/>
796 </when> 801 </when>
797 <when value="pl.diffmap"> 802 <when value="pl.diffmap">
798 <expand macro="param_color"/> 803 <expand macro="param_color"/>
804 <expand macro="param_gene_symbols"/>
799 <expand macro="param_use_raw"/> 805 <expand macro="param_use_raw"/>
800 <expand macro="param_sort_order"/> 806 <expand macro="param_sort_order"/>
801 <expand macro="param_groups"/> 807 <expand macro="param_groups"/>
802 <expand macro="params_pl_attribute_section"/> 808 <expand macro="params_pl_attribute_section"/>
803 <expand macro="params_scatter_outine"/> 809 <expand macro="params_scatter_outine"/>
1600 <param name="adata" value="pbmc68k_reduced.h5ad"/> 1606 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1601 <param name="format" value="pdf"/> 1607 <param name="format" value="pdf"/>
1602 <conditional name="method"> 1608 <conditional name="method">
1603 <param name="method" value="pl.pca"/> 1609 <param name="method" value="pl.pca"/>
1604 <param name="color" value="CD3D,CD79A"/> 1610 <param name="color" value="CD3D,CD79A"/>
1611 <param name="gene_symbols" value="symbol"/>
1605 <section name="plot"> 1612 <section name="plot">
1606 <repeat name="components"> 1613 <repeat name="components">
1607 <param name="axis1" value="1"/> 1614 <param name="axis1" value="1"/>
1608 <param name="axis2" value="2"/> 1615 <param name="axis2" value="2"/>
1609 </repeat> 1616 </repeat>
1635 <has_text_matching expression="size=1.0"/> 1642 <has_text_matching expression="size=1.0"/>
1636 <has_text_matching expression="frameon=True"/> 1643 <has_text_matching expression="frameon=True"/>
1637 <has_text_matching expression="ncols=2"/> 1644 <has_text_matching expression="ncols=2"/>
1638 <has_text_matching expression="wspace=0.1"/> 1645 <has_text_matching expression="wspace=0.1"/>
1639 <has_text_matching expression="hspace=0.25"/> 1646 <has_text_matching expression="hspace=0.25"/>
1647 <has_text_matching expression="gene_symbols='symbol'"/>
1640 </assert_contents> 1648 </assert_contents>
1641 </output> 1649 </output>
1642 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> 1650 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
1643 </test> 1651 </test>
1644 1652
1756 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> 1764 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
1757 <param name="format" value="png"/> 1765 <param name="format" value="png"/>
1758 <conditional name="method"> 1766 <conditional name="method">
1759 <param name="method" value="pl.umap"/> 1767 <param name="method" value="pl.umap"/>
1760 <param name="color" value="paul15_clusters"/> 1768 <param name="color" value="paul15_clusters"/>
1769 <param name="gene_symbols" value="symbol"/>
1761 <conditional name="edges"> 1770 <conditional name="edges">
1762 <param name="edges" value="True"/> 1771 <param name="edges" value="True"/>
1763 </conditional> 1772 </conditional>
1764 <section name="plot"> 1773 <section name="plot">
1765 <param name="legend_fontsize" value="1"/> 1774 <param name="legend_fontsize" value="1"/>
1786 <has_text_matching expression="size=1.0"/> 1795 <has_text_matching expression="size=1.0"/>
1787 <has_text_matching expression="frameon=True"/> 1796 <has_text_matching expression="frameon=True"/>
1788 <has_text_matching expression="ncols=4"/> 1797 <has_text_matching expression="ncols=4"/>
1789 <has_text_matching expression="wspace=0.1"/> 1798 <has_text_matching expression="wspace=0.1"/>
1790 <has_text_matching expression="hspace=0.25"/> 1799 <has_text_matching expression="hspace=0.25"/>
1791 1800 <has_text_matching expression="gene_symbols='symbol'"/>
1792 </assert_contents> 1801 </assert_contents>
1793 </output> 1802 </output>
1794 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1803 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1795 </test> 1804 </test>
1796 1805
1799 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 1808 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1800 <param name="format" value="png"/> 1809 <param name="format" value="png"/>
1801 <conditional name="method"> 1810 <conditional name="method">
1802 <param name="method" value="pl.diffmap"/> 1811 <param name="method" value="pl.diffmap"/>
1803 <param name="color" value="paul15_clusters"/> 1812 <param name="color" value="paul15_clusters"/>
1813 <param name="gene_symbols" value="symbol"/>
1804 <section name="plot"> 1814 <section name="plot">
1805 <param name="legend_fontsize" value="1"/> 1815 <param name="legend_fontsize" value="1"/>
1806 <param name="legend_fontweight" value="normal"/> 1816 <param name="legend_fontweight" value="normal"/>
1807 <param name="size" value="1"/> 1817 <param name="size" value="1"/>
1808 </section> 1818 </section>
1823 <has_text_matching expression="size=1.0"/> 1833 <has_text_matching expression="size=1.0"/>
1824 <has_text_matching expression="frameon=True"/> 1834 <has_text_matching expression="frameon=True"/>
1825 <has_text_matching expression="ncols=4"/> 1835 <has_text_matching expression="ncols=4"/>
1826 <has_text_matching expression="wspace=0.1"/> 1836 <has_text_matching expression="wspace=0.1"/>
1827 <has_text_matching expression="hspace=0.25"/> 1837 <has_text_matching expression="hspace=0.25"/>
1828 1838 <has_text_matching expression="gene_symbols='symbol'"/>
1829 </assert_contents> 1839 </assert_contents>
1830 </output> 1840 </output>
1831 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1841 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1832 </test> 1842 </test>
1833 1843