From 391b09102384ce6c0c96bc9ea7668bb0db8dabfa Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 29 Nov 2019 19:15:12 +0100
Subject: [PATCH 1/3] Fix scanpy by using profile

---
 tools/scanpy/cluster_reduce_dimension.xml | 2 +-
 tools/scanpy/filter.xml                   | 2 +-
 tools/scanpy/inspect.xml                  | 2 +-
 tools/scanpy/macros.xml                   | 1 +
 tools/scanpy/normalize.xml                | 2 +-
 tools/scanpy/plot.xml                     | 2 +-
 tools/scanpy/remove_confounders.xml       | 2 +-
 7 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/tools/scanpy/cluster_reduce_dimension.xml b/tools/scanpy/cluster_reduce_dimension.xml
index bd12cc1d290..c739ecab2f3 100644
--- a/tools/scanpy/cluster_reduce_dimension.xml
+++ b/tools/scanpy/cluster_reduce_dimension.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@">
+<tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@" profile="@profile@">
     <description>infer trajectories and embed with scanpy</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/scanpy/filter.xml b/tools/scanpy/filter.xml
index 83004c3631a..871e1624229 100644
--- a/tools/scanpy/filter.xml
+++ b/tools/scanpy/filter.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_filter" name="Filter" version="@galaxy_version@">
+<tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@">
     <description>with scanpy</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/scanpy/inspect.xml b/tools/scanpy/inspect.xml
index c8c418c82a9..ff93c2bd99b 100644
--- a/tools/scanpy/inspect.xml
+++ b/tools/scanpy/inspect.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@">
+<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/scanpy/macros.xml b/tools/scanpy/macros.xml
index 68f2238da62..0ed2e0a5563 100644
--- a/tools/scanpy/macros.xml
+++ b/tools/scanpy/macros.xml
@@ -1,5 +1,6 @@
 <macros>
     <token name="@version@">1.4.4</token>
+    <token name="@profile@">19.01</token>
     <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/scanpy/normalize.xml b/tools/scanpy/normalize.xml
index 6d381efd0db..d90c119cd60 100644
--- a/tools/scanpy/normalize.xml
+++ b/tools/scanpy/normalize.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@">
+<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
     <description>with scanpy</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/scanpy/plot.xml b/tools/scanpy/plot.xml
index 0b205444b9e..4784f67c08e 100644
--- a/tools/scanpy/plot.xml
+++ b/tools/scanpy/plot.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_plot" name="Plot" version="@galaxy_version@">
+<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/scanpy/remove_confounders.xml b/tools/scanpy/remove_confounders.xml
index a9130029922..95a2d3e4b89 100644
--- a/tools/scanpy/remove_confounders.xml
+++ b/tools/scanpy/remove_confounders.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@">
+<tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@" profile="@profile@">
     <description>with scanpy</description>
     <macros>
         <import>macros.xml</import>

From 8573e8a765be1a0c1b113100183c042869200261 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 30 Nov 2019 18:48:31 +0100
Subject: [PATCH 2/3] Bump scanpy to 1.4.4.post1 which includes louvain
 depencency

---
 tools/scanpy/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scanpy/macros.xml b/tools/scanpy/macros.xml
index 0ed2e0a5563..95641860419 100644
--- a/tools/scanpy/macros.xml
+++ b/tools/scanpy/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@version@">1.4.4</token>
+    <token name="@version@">1.4.4.post1</token>
     <token name="@profile@">19.01</token>
     <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
     <xml name="requirements">

From 07c6c3b7787e9d7c2311eb0cdcb2def4e5b1c4b2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 2 Dec 2019 13:05:03 +0100
Subject: [PATCH 3/3] Add louvain dependency to
 scanpy/cluster_reduce_dimension.xml

---
 tools/scanpy/cluster_reduce_dimension.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tools/scanpy/cluster_reduce_dimension.xml b/tools/scanpy/cluster_reduce_dimension.xml
index c739ecab2f3..9ab98b3117f 100644
--- a/tools/scanpy/cluster_reduce_dimension.xml
+++ b/tools/scanpy/cluster_reduce_dimension.xml
@@ -58,7 +58,9 @@ This data is accessible using the inspect tool for AnnData
     use_highly_variable=$method.use_highly_variable
 ]]></token>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="0.6.1">louvain</requirement>
+    </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@