Mercurial > repos > iuc > scanpy_plot

changeset 8:6adf98e782f3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
author iuc
date Tue, 16 Mar 2021 13:01:04 +0000
parents 7647e5cd1b8b
children 9a169729c9f9
files 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
diffstat 11 files changed, 11 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed May 20 16:08:18 2020 -0400
+++ b/macros.xml	Tue Mar 16 13:01:04 2021 +0000
@@ -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=$method.seaborn_violinplot.saturation
     ]]></token>
     <xml name="param_color">
@@ -1005,7 +997,7 @@
         <option value="eq_tree">eq_tree: Equally spaced tree</option>
     </xml>
     <xml name="param_layout">
-        <param argument="layout" type="select" label="Plotting layout" help="">
+        <param argument="layout" type="select" label="Plotting layout" optional="false" help="">
             <expand macro="options_layout"/>
         </param>
     </xml>
--- a/plot.xml	Wed May 20 16:08:18 2020 -0400
+++ b/plot.xml	Tue Mar 16 13:01:04 2021 +0000
@@ -45,7 +45,7 @@
     projection='$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>
Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed
Binary file test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png has changed
Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed
Binary file test-data/pl.stacked_violin.krumsiek11.png has changed
Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed
Binary file test-data/pp.highly_variable_genes.seurat.blobs.h5ad has changed
Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed
Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed
Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed