diff macros.xml @ 11:95777145cb92 draft

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

--- a/macros.xml	Wed Sep 22 21:13:39 2021 +0000
+++ b/macros.xml	Wed Nov 08 14:47:20 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) != ''