# HG changeset patch
# User iuc
# Date 1651953314 0
# Node ID 05631436cdf18e9a003954bea2e56dd2c6e16a55
# Parent  7784821452ac15d79f93ec5aa173598b1fbfe67b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"

diff -r 7784821452ac -r 05631436cdf1 macros.xml
--- a/macros.xml	Fri Feb 19 23:53:44 2021 +0000
+++ b/macros.xml	Sat May 07 19:55:14 2022 +0000
@@ -46,7 +46,7 @@
 and machine learning packages in Python (statsmodels, scikit-learn).
 
 More details on the `AnnData documentation
-<https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
+<https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.html>`__
 
 
 **Loom data**
diff -r 7784821452ac -r 05631436cdf1 modify_loom.xml
--- a/modify_loom.xml	Fri Feb 19 23:53:44 2021 +0000
+++ b/modify_loom.xml	Sat May 07 19:55:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+@GALAXY_VERSION@">
+<tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+galaxy1">
     <description>Add layers, or row/column attributes to a loom file</description>
     <macros>
         <import>macros.xml</import>
@@ -6,7 +6,8 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/modify_loom.py' -f '${input}'
+cp '${input}' loom_add_out.loom &&
+python '$__tool_directory__/modify_loom.py' -f 'loom_add_out.loom'
 #if $which_add.add_type == "cols":
     -a cols -c '${which_add.cols}'
 #else if $which_add.add_type == "cols":
@@ -14,7 +15,6 @@
 #else if $which_add.add_type == "layers":
     -a layers -l '${which_add.layers}'
 #end if
-&& cp '${input}' loom_add_out.loom
       ]]></command>
     <inputs>
         <param name="input" type="data" format="loom" label="Loom file"/>