--- a/import.xml	Wed Jul 22 12:21:43 2020 -0400
+++ b/import.xml	Thu Jan 07 23:28:53 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="18.01">
+<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="20.09">
     <description>from different format</description>
     <macros>
         <import>macros.xml</import>
@@ -58,7 +58,7 @@
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
 #if $hd5_format.filetype == 'anndata'
-#if $hd5_format.in.adata_format == 'loom'
+    #if $hd5_format.in.adata_format == 'loom'
 adata = ad.read_loom(
     '$hd5_format.in.input',
     sparse=$hd5_format.in.sparse,
@@ -67,24 +67,24 @@
     obs_names='$hd5_format.in.obs_names',
     var_names='$hd5_format.in.var_names')
 
-#else if $hd5_format.in.adata_format == 'tabular'
-    #set delimiter=$hd5_format.in.input.metadata.delimiter
-    #if $delimiter != ','
-        #set delimiter='\\t'
-    #end if
+    #else if $hd5_format.in.adata_format == 'tabular'
+        #set delimiter=$hd5_format.in.input.metadata.delimiter
+        #if $delimiter != ','
+            #set delimiter='\\t'
+        #end if
 adata = ad.read_csv(
     '$hd5_format.in.input',
     delimiter='$delimiter',
     first_column_names=$hd5_format.in.first_column_names)
 
-#else if $hd5_format.in.adata_format == '10x_h5'
+    #else if $hd5_format.in.adata_format == '10x_h5'
 import scanpy as sc
 adata = sc.read_10x_h5('$hd5_format.in.input')
 
-#else if $hd5_format.in.adata_format == 'mtx'
-    #if $hd5_format.in.tenx.use == 'no'
+    #else if $hd5_format.in.adata_format == 'mtx'
+        #if $hd5_format.in.tenx.use == 'no'
 adata = ad.read_mtx(filename='$hd5_format.in.matrix')
-    #else
+        #else
 import scanpy as sc
 adata = sc.read_10x_mtx(
     'mtx',
@@ -92,12 +92,11 @@
     make_unique=$hd5_format.in.tenx.make_unique,
     cache=False,
     gex_only=$hd5_format.in.tenx.gex_only)
-    #end if
+        #end if
 
-#else if $hd5_format.in.adata_format == 'umi_tools'
+    #else if $hd5_format.in.adata_format == 'umi_tools'
 adata = ad.read_umi_tools('${hd5_format.in.input}.gz')
-
-#end if
+    #end if
 adata.write('anndata.h5ad')
 #end if
 ]]></configfile>
@@ -176,7 +175,7 @@
         <test expect_num_outputs="1">
             <conditional name="in">
                 <param name="adata_format" value="loom"/>
-                <param name="input" value="krumsiek11.loom" />
+                <param name="input" ftype="loom" value="krumsiek11.loom" />
                 <param name="sparse" value="True"/>
                 <param name="cleanup" value="False"/>
                 <param name="x_name"  value="spliced"/>
@@ -219,7 +218,7 @@
             </assert_stdout>
             <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <!--<test expect_num_outputs="1">
+        <test expect_num_outputs="1">
             <conditional name="in">
                 <param name="adata_format" value="mtx"/>
                 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
@@ -229,7 +228,7 @@
                 </conditional>
             <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
+        <!--<test>
             <conditional name="in">
                 <param name="adata_format" value="mtx"/>
                 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
@@ -293,6 +292,7 @@
         </test>
     </tests>
     <help><![CDATA[
+
 **What it does**
 
 This tool creates an AnnData or loom dataset from several input types: