Mercurial > repos > iuc > scanpy_filter

changeset 8:f87ed6503715 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 13:00:13 +0000
parents 3c86f71498bc
children 5511647110ff
files filter.xml macros.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, 7 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/filter.xml	Wed May 20 16:12:00 2020 -0400
+++ b/filter.xml	Tue Mar 16 13:00:13 2021 +0000
@@ -350,7 +350,7 @@
                     <has_text_matching expression="subset=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/>
         </test>
         <test>
             <!-- test 5 -->
@@ -376,7 +376,7 @@
                     <has_text_matching expression="subset=True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/>
         </test>
         <test>
             <!-- test 6 -->
@@ -444,7 +444,7 @@
                     <has_text_matching expression="replace=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="10000000" delta_frac="0.5"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Wed May 20 16:12:00 2020 -0400
+++ b/macros.xml	Tue Mar 16 13:00:13 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>
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