| Previous changeset 7:7647e5cd1b8b (2020-05-20) Next changeset 9:9a169729c9f9 (2021-04-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" |
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modified:
macros.xml plot.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png test-data/pl.scatter.umap.pbmc68k_reduced.png test-data/pl.stacked_violin.krumsiek11.png test-data/pl.violin.pbmc68k_reduced_custom.png test-data/pp.highly_variable_genes.seurat.blobs.h5ad test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_zheng17.random-randint.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad |
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| diff -r 7647e5cd1b8b -r 6adf98e782f3 macros.xml --- a/macros.xml Wed May 20 16:08:18 2020 -0400 +++ b/macros.xml Tue Mar 16 13:01:04 2021 +0000 |
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| @@ -1,13 +1,12 @@ <macros> - <token name="@version@">1.4.4.post1</token> + <token name="@version@">1.7.1</token> <token name="@profile@">19.01</token> - <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></token> + <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@version@">scanpy</requirement> <requirement type="package" version="2.0.17">loompy</requirement> - <requirement type="package" version="2.9.0">h5py</requirement> - <requirement type="package" version="0.7.0">leidenalg</requirement> + <requirement type="package" version="0.8.3">leidenalg</requirement> <yield /> </requirements> </xml> @@ -29,9 +28,6 @@ ]]> </token> <token name="@CMD_imports@"><![CDATA[ -import sys -sys.stderr = open('$hidden_output', 'a') - import scanpy as sc import pandas as pd import numpy as np @@ -768,9 +764,6 @@ <param argument="color" type="select" label="Color for all of the elements" help=""> <expand macro="matplotlib_color"/> </param> - <param argument="palette" type="select" label="Colors to use for the different levels of the hue variable" help=""> - <expand macro="matplotlib_pyplot_colormap"/> - </param> <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> </section> </xml> @@ -781,7 +774,6 @@ #end if linewidth=$method.seaborn_violinplot.linewidth, color='$method.seaborn_violinplot.color', - palette='$method.seaborn_violinplot.palette', saturation=$method.seaborn_violinplot.saturation ]]></token> <xml name="param_color"> @@ -1005,7 +997,7 @@ <option value="eq_tree">eq_tree: Equally spaced tree</option> </xml> <xml name="param_layout"> - <param argument="layout" type="select" label="Plotting layout" help=""> + <param argument="layout" type="select" label="Plotting layout" optional="false" help=""> <expand macro="options_layout"/> </param> </xml> |
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| diff -r 7647e5cd1b8b -r 6adf98e782f3 plot.xml --- a/plot.xml Wed May 20 16:08:18 2020 -0400 +++ b/plot.xml Tue Mar 16 13:01:04 2021 +0000 |
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| @@ -45,7 +45,7 @@ projection='$method.plot.projection', legend_loc='$method.plot.legend_loc', #if $method.plot.palette != 'default' - palette='$method.plot.palette', + palette=['$method.plot.palette'], #end if #if $method.plot.color_map != 'None' color_map='$method.plot.color_map', @@ -239,9 +239,7 @@ gene_symbols='$method.gene_symbols', #end if use_raw=$method.use_raw, - #if str($method.layout) != 'None' layout='$method.layout', - #end if edges=$method.edges.edges, #if str($method.edges.edges) == 'True' edges_width=$method.edges.edges_width, @@ -404,7 +402,9 @@ <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option> <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option> <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option> + <!-- doesn't currenty work: https://github.com/galaxyproject/tools-iuc/pull/3485#issuecomment-800055967 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option> + --> <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option> <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option> <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option> @@ -639,7 +639,7 @@ <expand macro="param_color"/> <expand macro="gene_symbols"/> <expand macro="param_use_raw"/> - <param argument="layout" type="select" optional="true" label="Plotting layout" help=""> + <param argument="layout" type="select" optional="false" label="Plotting layout" help=""> <expand macro="options_layout"/> </param> <expand macro="pl_edges"/> @@ -814,7 +814,6 @@ <has_text_matching expression="legend_fontsize=1"/> <has_text_matching expression="legend_fontweight='normal'"/> <has_text_matching expression="color_map='inferno'"/> - <has_text_matching expression="palette='inferno'"/> <has_text_matching expression="frameon=True"/> <has_text_matching expression="size=1.0"/> </assert_contents> @@ -862,7 +861,6 @@ <has_text_matching expression="legend_loc='right margin'"/> <has_text_matching expression="legend_fontsize=1"/> <has_text_matching expression="legend_fontweight='normal'"/> - <has_text_matching expression="palette='bwr'"/> <has_text_matching expression="frameon=False"/> <has_text_matching expression="size=1.0"/> <has_text_matching expression="title='A title'"/> @@ -1029,7 +1027,6 @@ <has_text_matching expression="scale='width'"/> <has_text_matching expression="linewidth=0.0"/> <has_text_matching expression="color='AliceBlue'"/> - <has_text_matching expression="palette='viridis'"/> <has_text_matching expression="saturation=0.75"/> </assert_contents> </output> @@ -1067,7 +1064,6 @@ <param name="bw" value="scott"/> <param name="linewidth" value="0"/> <param name="color" value="AliceBlue"/> - <param name="palette" value="viridis"/> <param name="saturation" value="0.75"/> </section> </conditional> @@ -1091,7 +1087,6 @@ <has_text_matching expression="scale='width'"/> <has_text_matching expression="linewidth=0.0"/> <has_text_matching expression="color='AliceBlue'"/> - <has_text_matching expression="palette='viridis'"/> <has_text_matching expression="saturation=0.75"/> </assert_contents> </output> @@ -1539,6 +1534,7 @@ <conditional name="method"> <param name="method" value="pl.draw_graph"/> <param name="use_raw" value="false"/> + <param name="layout" value="fr"/> <conditional name="edges"> <param name="edges" value="True"/> <param name="edges_width" value="0.1"/> @@ -1679,8 +1675,8 @@ </output> <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> </test> + <!-- test 20: pl.rank_genes_groups_violin, currently broken <test> - <!-- test 20: pl.rank_genes_groups_violin !--> <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1723,6 +1719,7 @@ <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> </output_collection> </test> + --> <test> <!-- test 21: pl.rank_genes_groups_dotplot !--> <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> @@ -1875,7 +1872,6 @@ <has_text_matching expression="scale='width'"/> <has_text_matching expression="linewidth=0.0"/> <has_text_matching expression="color='AliceBlue'"/> - <has_text_matching expression="palette='viridis'"/> <has_text_matching expression="saturation=0.75"/> </assert_contents> </output> |
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