diff manipulate.xml @ 2:a56baceb1900 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"

--- a/manipulate.xml	Wed Oct 16 06:26:45 2019 -0400
+++ b/manipulate.xml	Thu Dec 12 09:22:35 2019 -0500
@@ -120,6 +120,10 @@
     #else if $manipulate.var_obs == 'obs'
 adata = adata[filtered, :]
     #end if
+
+#else if $manipulate.function == 'save_raw'
+adata.raw = adata
+
 #end if
 
 adata.write('anndata.h5ad')
@@ -137,6 +141,7 @@
                 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
                 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
                 <option value="filter">Filter observations or variables</option>
+                <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
             </param>
             <when value="concatenate">
                 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
@@ -173,7 +178,7 @@
                     help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
             </when>
             <when value="filter">
-                <param name="var_obs" type="select" label="What to annotate?">
+                <param name="var_obs" type="select" label="What to filter?">
                     <option value="var">Variables (var)</option>
                     <option value="obs">Observations (obs)</option>
                 </param>
@@ -368,6 +373,14 @@
             </conditional>
             <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
+        <test>
+            <!-- test 11 -->
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="manipulate">
+                <param name="function" value="save_raw"/>
+            </conditional>
+            <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
@@ -406,6 +419,8 @@
 
 - Filter data variables or observations, by index or key
 
+- Freeze the current state into the 'raw' attribute
+
 @HELP@
     ]]></help>
     <expand macro="citations"/>