# HG changeset patch
# User iuc
# Date 1615899562 0
# Node ID 9d33775ec67d04f2cbe3145a06be4edff9f94d11
# Parent  6c145a6868ccbf1b6b7b02afb0e9420f402dcac9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"

diff -r 6c145a6868cc -r 9d33775ec67d inspect.xml
--- a/inspect.xml	Wed May 20 16:10:30 2020 -0400
+++ b/inspect.xml	Tue Mar 16 12:59:22 2021 +0000
@@ -232,12 +232,12 @@
 
 #else if $method.method == "pp.log1p"
 sc.pp.log1p(
-    data=adata,
+    adata,
     copy=False)
 
 #else if $method.method == "pp.scale"
 sc.pp.scale(
-    data=adata,
+    adata,
     zero_center=$method.zero_center,
     #if $method.max_value
     max_value=$method.max_value,
@@ -246,7 +246,7 @@
 
 #else if $method.method == "pp.sqrt"
 sc.pp.sqrt(
-    data=adata,
+    adata,
     copy=False)
 #end if
 
@@ -707,9 +707,9 @@
                     <has_text_matching expression="C=1.0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size">
+            <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15">
                 <assert_contents>
-                    <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
+                    <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" />
                 </assert_contents>
             </output>
         </test>
@@ -762,9 +762,9 @@
                     <has_text_matching expression="C=1.0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size">
+            <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15">
                 <assert_contents>
-                    <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
+                    <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" />
                 </assert_contents>
             </output>
         </test>
diff -r 6c145a6868cc -r 9d33775ec67d macros.xml
--- a/macros.xml	Wed May 20 16:10:30 2020 -0400
+++ b/macros.xml	Tue Mar 16 12:59:22 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>
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pl.scatter.umap.pbmc68k_reduced.png
Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pl.stacked_violin.krumsiek11.png
Binary file test-data/pl.stacked_violin.krumsiek11.png has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pl.violin.pbmc68k_reduced_custom.png
Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pp.highly_variable_genes.seurat.blobs.h5ad
Binary file test-data/pp.highly_variable_genes.seurat.blobs.h5ad has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pp.recipe_seurat.recipe_zheng17.h5ad
Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/pp.recipe_zheng17.random-randint.h5ad
Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed
diff -r 6c145a6868cc -r 9d33775ec67d test-data/tl.rank_genes_groups.krumsiek11.h5ad
Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed