# HG changeset patch
# User iuc
# Date 1615899822 0
# Node ID 35bc2eb568ed59460952bbac58d2b3cd5c423d74
# Parent  b2df381a6004bc632b4837cf137afd3afa1e378c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"

diff -r b2df381a6004 -r 35bc2eb568ed cluster_reduce_dimension.xml
--- a/cluster_reduce_dimension.xml	Wed May 20 16:11:15 2020 -0400
+++ b/cluster_reduce_dimension.xml	Tue Mar 16 13:03:42 2021 +0000
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
         <xml name="pca_inputs">
-            <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/>
+            <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/>
             <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help="">
                 <expand macro="sanitize_query" />
             </param>
@@ -46,7 +46,7 @@
 ]]></token>
         <token name="@CMD_pca_params@"><![CDATA[
     data=adata,
-    n_comps=$method.n_comps,
+    n_comps=min($method.n_comps, adata.n_vars),
     dtype='$method.dtype',
     copy=False,
     chunked=$method.pca.chunked,
@@ -61,7 +61,7 @@
 ]]></token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.6.1">louvain</requirement>
+        <requirement type="package" version="0.7.0">louvain</requirement>
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -104,7 +104,7 @@
 #else if $method.method == 'tl.diffmap'
 sc.tl.diffmap(
     adata=adata,
-    n_comps=$method.n_comps,
+    n_comps=min($method.n_comps, adata.n_vars),
     copy =False)
 
 #else if $method.method == 'tl.tsne'
@@ -372,7 +372,6 @@
             <output name="hidden_output">
                 <assert_contents>
                     <has_text_matching expression="sc.pp.pca"/>
-                    <has_text_matching expression="n_comps=50"/>
                     <has_text_matching expression="dtype='float32'"/>
                     <has_text_matching expression="copy=False"/>
                     <has_text_matching expression="chunked=False"/>
@@ -382,7 +381,7 @@
                     <has_text_matching expression="use_highly_variable=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
         </test>
         <!--<test>
             < test 3 >
@@ -431,7 +430,6 @@
             <output name="hidden_output">
                 <assert_contents>
                     <has_text_matching expression="sc.tl.pca"/>
-                    <has_text_matching expression="n_comps=50"/>
                     <has_text_matching expression="dtype='float32'"/>
                     <has_text_matching expression="copy=False"/>
                     <has_text_matching expression="chunked=False"/>
@@ -440,7 +438,7 @@
                     <has_text_matching expression="use_highly_variable=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
         </test>
         <test>
             <!-- test 3 -->
@@ -455,7 +453,6 @@
             <output name="hidden_output">
                 <assert_contents>
                     <has_text_matching expression="sc.tl.diffmap"/>
-                    <has_text_matching expression="n_comps=15"/>
                 </assert_contents>
             </output>
             <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
diff -r b2df381a6004 -r 35bc2eb568ed macros.xml
--- a/macros.xml	Wed May 20 16:11:15 2020 -0400
+++ b/macros.xml	Tue Mar 16 13:03:42 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 b2df381a6004 -r 35bc2eb568ed 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 b2df381a6004 -r 35bc2eb568ed 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 b2df381a6004 -r 35bc2eb568ed test-data/pl.scatter.umap.pbmc68k_reduced.png
Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/pl.stacked_violin.krumsiek11.png
Binary file test-data/pl.stacked_violin.krumsiek11.png has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/pl.violin.pbmc68k_reduced_custom.png
Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/pp.highly_variable_genes.seurat.blobs.h5ad
Binary file test-data/pp.highly_variable_genes.seurat.blobs.h5ad has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/pp.recipe_seurat.recipe_zheng17.h5ad
Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/pp.recipe_zheng17.random-randint.h5ad
Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed
diff -r b2df381a6004 -r 35bc2eb568ed test-data/tl.rank_genes_groups.krumsiek11.h5ad
Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed