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Changeset 11:c9cb76cf8d6c (2023-11-08)

Previous changeset 10:ab55fe8030b6 (2021-09-22) Next changeset 12:94c19fb1281c (2023-11-17)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d

added:
test-data/pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png
test-data/pl.embedding_density.pbmc68k_reduced.png
test-data/pl.paga_compare.paul15_gauss_braycurtis.png
test-data/pl.scatter.pbmc68k_reduced.png
test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad
test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad
test-data/tl.paga.neighbors.paul15_gauss_braycurtis.h5ad

diff -r ab55fe8030b6 -r c9cb76cf8d6c macros.xml
--- a/macros.xml Wed Sep 22 21:12:45 2021 +0000
+++ b/macros.xml Wed Nov 08 14:49:18 2023 +0000

[

@@ -1,12 +1,16 @@
<macros>
-    <token name="@version@">1.7.1</token>
-    <token name="@profile@">19.01</token>
+    <token name="@version@">1.9.6</token>
+    <token name="@profile@">22.05</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="0.8.3">leidenalg</requirement>
+            <requirement type="package" version="3.0.6">loompy</requirement>
+            <requirement type="package" version="0.10.1">leidenalg</requirement>
+            <requirement type="package" version="0.8.1">louvain</requirement>
+            <requirement type="package" version="1.5.3">pandas</requirement>
+            <requirement type="package" version="3.7">matplotlib</requirement>
+            <requirement type="package" version="0.12.2">seaborn</requirement>
             <yield />
         </requirements>
     </xml>
@@ -15,9 +19,15 @@
             <xref type="bio.tools">scanpy</xref>
         </xrefs>
     </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-017-1382-0</citation>
+            <citation type="doi">10.1093/gigascience/giaa102</citation>
         </citations>
     </xml>
     <xml name="version_command">
@@ -56,7 +66,7 @@
         <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
     </xml>
     <token name="@CMD_read_inputs@"><![CDATA[
-adata = sc.read('anndata.h5ad')
+adata = sc.read_h5ad('anndata.h5ad')
]]>
     </token>
     <xml name="inputs_common_advanced">
@@ -66,12 +76,12 @@
     </xml>
     <xml name="anndata_outputs">
         <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
-        <data name="hidden_output" format="txt" label="Log file" >
+            <data name="hidden_output" format="txt" label="Log file" >
             <filter>advanced_common['show_log']</filter>
         </data>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
-adata.write('anndata.h5ad')
+adata.write_h5ad('anndata.h5ad')
with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
     print(adata, file=ainfo)
]]>
@@ -875,7 +885,7 @@
     </xml>
     <xml name="param_color_map">
         <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
-            <option value="None">Default</option>
+            <option value="" >Default</option>
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -979,7 +989,7 @@
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
     @CMD_param_size@
-    #if str($method.plot.color_map) != 'None'
+    #if str($method.plot.color_map) != ''
     color_map='$method.plot.color_map',
     #end if
     #if str($method.plot.palette) != ''

diff -r ab55fe8030b6 -r c9cb76cf8d6c normalize.xml
--- a/normalize.xml Wed Sep 22 21:12:45 2021 +0000
+++ b/normalize.xml Wed Nov 08 14:49:18 2023 +0000

[

@@ -1,9 +1,9 @@
<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
     <description>with scanpy</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -126,8 +126,8 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
-            
+        <test expect_num_outputs="2">
+            
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.normalize_total"/>
@@ -151,8 +151,8 @@
             </output>
             <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            
+        <test expect_num_outputs="2">
+            
             <param name="adata" value="random-randint.h5ad"/>
             <conditional name="method">
                 <param name="method" value="pp.recipe_zheng17"/>
@@ -171,8 +171,8 @@
             </output>
             <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/>
         </test>
-        <test>
-            
+        <test expect_num_outputs="2">
+            
             <param name="adata" value="paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.recipe_weinreb17"/>
@@ -199,8 +199,8 @@
             </output>
             <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            
+        <test expect_num_outputs="2">
+            
             <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.recipe_seurat"/>
@@ -228,7 +228,7 @@
Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.

More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.normalize_per_cell.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__

Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
@@ -247,7 +247,7 @@
- scale to unit variance and shift to zero mean

More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_zheng17.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__

Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
@@ -256,7 +256,7 @@
Expects non-logarithmized data. If using logarithmized data, pass `log=False`.

More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_weinreb17.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__

Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
@@ -267,7 +267,7 @@
Expects non-logarithmized data. If using logarithmized data, pass `log=False`.

More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_seurat.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__

     ]]></help>
     <expand macro="citations"/>

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