Fix to SCEasy tool (galaxyproject#5674)

* better help tags * Fix to macros * anndata from h5 to h5ad Thanks to @wee-snufkin for reporting * test fix * removed comments
bernt-matthias · Dec 12, 2023 · 49fa5e8 · 49fa5e8
1 parent cb8c315
commit 49fa5e8
Showing 1 changed file with 15 additions and 15 deletions.
diff --git a/tools/sceasy/sceasy.xml b/tools/sceasy/sceasy.xml
@@ -4,7 +4,7 @@
     </description>
     <macros>
         <token name="@TOOL_VERSION@">0.0.7</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <macro name="mac_input_form" token_format="@FORMAT@" >
             <param name="input_object_file" type="data" format="@FORMAT@" label="Input object in @FORMAT@ format"/>
         </macro>
@@ -110,28 +110,28 @@ if (do_infile_as_first_arg) {
                 <option value="seurat2sce" >Seurat to SingleCellexperiment</option>
             </param>
             <when value="anndata2cds" >
-                <expand macro="mac_input_form" token_format="h5ad" />
+                <expand macro="mac_input_form" format="h5ad,h5" />
             </when>
             <when value="anndata2seurat" >
-                <expand macro="mac_input_form" token_format="h5ad" />
+                <expand macro="mac_input_form" format="h5ad,h5" />
             </when>
             <when value="loom2anndata">
-                <expand macro="mac_input_form" token_format="h5" />
+                <expand macro="mac_input_form" format="h5,loom,rdata" />
             </when>
             <when value="loom2sce">
-                <expand macro="mac_input_form" token_format="h5" />
+                <expand macro="mac_input_form" format="h5,loom,rdata" />
             </when>
             <when value="sce2anndata">
-                <expand macro="mac_input_form" token_format="sce" />
+                <expand macro="mac_input_form" format="sce,rds,rdata.sce" />
             </when>
             <when value="sce2loom">
-                <expand macro="mac_input_form" token_format="sce" />
+                <expand macro="mac_input_form" format="sce,rds,rdata.sce" />
             </when>
             <when value="seurat2anndata">
-                <expand macro="mac_input_form" token_format="rds" />
+                <expand macro="mac_input_form" format="rds,rdata" />
             </when>
             <when value="seurat2sce">
-                <expand macro="mac_input_form" token_format="rds" />
+                <expand macro="mac_input_form" format="rds,rdata" />
             </when>
         </conditional>
     </inputs>
@@ -151,7 +151,7 @@ if (do_infile_as_first_arg) {
                 conversion['direction'].endswith('loom')
             </filter>
         </data>
-        <data name="output_anndata" format="h5" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData">
+        <data name="output_anndata" format="h5ad" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData">
             <filter>
                 conversion['direction'].endswith('anndata')
             </filter>
@@ -176,7 +176,7 @@ if (do_infile_as_first_arg) {
         <test expect_num_outputs="1">
             <param name="direction" value="loom2anndata"/>
             <param name="input_object_file" value="sce2loom.rds"/>
-            <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5" compare="sim_size"/>
+            <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="direction" value="loom2sce"/>
@@ -186,7 +186,7 @@ if (do_infile_as_first_arg) {
         <test expect_num_outputs="1">
             <param name="direction" value="sce2anndata"/>
             <param name="input_object_file" value="test_sce.rds"/>
-            <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5" compare="sim_size"/>
+            <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="direction" value="sce2loom"/>
@@ -196,15 +196,15 @@ if (do_infile_as_first_arg) {
         <test expect_num_outputs="1">
             <param name="direction" value="seurat2anndata"/>
             <param name="input_object_file" value="test_seurat.rds"/>
-            <output name="output_seurat" file="test_anndata.h5ad" ftype="h5" compare="sim_size"/>
+            <output name="output_anndata" file="test_anndata.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="direction" value="seurat2sce"/>
             <param name="input_object_file" value="test_seurat.rds"/>
             <output name="output_sce" file="test_sce.rds" ftype="rdata" compare="sim_size"/>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 SCeasy
 ======
 
@@ -217,7 +217,7 @@ Supports the following conversion:
 	:align: center
 
 
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi"> doi:10.1093/nargab/lqaa052</citation>
     </citations>