Merge pull request #2704 from mvdbeek/fix_scanpy

Fix scanpy by using profile
galaxyproject · Dec 5, 2019 · e6675ef · e6675ef
2 parents c845cb2 + 07c6c3b
commit e6675ef
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Showing 7 changed files with 11 additions and 8 deletions.
diff --git 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>
@@ -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@

diff --git 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
@@ -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
@@ -1,5 +1,6 @@
 <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">
         <requirements>

diff --git 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
@@ -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
@@ -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>