Merge pull request galaxyproject#7504 from pavanvidem/scanpy-plot-out-h5ad

Scanpy plot add an option to output anndata

Author: bgruening

tools/scanpy/filter.xml

@@ -1,4 +1,4 @@
-<tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
+<tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>mark and subsample</description>
     <macros>
         <import>macros.xml</import>

tools/scanpy/inspect.xml

@@ -1,4 +1,4 @@
-<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <macros>
         <import>macros.xml</import>
         <xml name="params_score_genes">

tools/scanpy/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.2</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
@@ -53,6 +53,7 @@
     <xml name="inputs_common_advanced">
         <section name="advanced_common" title="Advanced Options" expanded="false">
             <param name="show_log" type="boolean" checked="false" label="Output Log?"/>
+            <yield />
         </section>
     </xml>
     <xml name="anndata_outputs">

tools/scanpy/plot.xml

@@ -369,8 +369,6 @@ sc.pl.paga(
     @CMD_PARAMS_PL_PAGA@
     @CMD_SHOW_NONE@)
 
-@CMD_ANNDATA_WRITE_OUTPUTS@
-
 #else if str($method.method) == 'pl.paga_compare':
 sc.pl.paga_compare(
     @CMD_PARAM_PLOT_INPUTS@
@@ -505,6 +503,11 @@ sc.pl.rank_genes_groups_tracksplot(
     @CMD_SHOW_NONE@)
 
 #end if
+
+#if $advanced_common.output_anndata:
+@CMD_ANNDATA_WRITE_OUTPUTS@
+#end if
+
 ]]></configfile>
     </configfiles>
     <inputs>
@@ -975,7 +978,9 @@ sc.pl.rank_genes_groups_tracksplot(
                 <expand macro="params_pl_heatmap"/>
             </when>
         </conditional>
-        <expand macro="inputs_common_advanced"/>
+        <expand macro="inputs_common_advanced">
+            <param name="output_anndata" type="boolean" checked="false" label="Output annotated data matrix?"/>
+        </expand>
     </inputs>
     <outputs>
         <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
@@ -1003,7 +1008,7 @@ sc.pl.rank_genes_groups_tracksplot(
             <filter>advanced_common['show_log']</filter>
         </data>
         <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
-            <filter>method['method'] == 'pl.paga'</filter>
+            <filter>advanced_common['output_anndata']</filter>
         </data>
     </outputs>
     <tests>
@@ -1755,7 +1760,7 @@ sc.pl.rank_genes_groups_tracksplot(
         </test>
 
         <!-- test 23 -->
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <param name="format" value="png"/>
             <conditional name="method">
@@ -1773,6 +1778,7 @@ sc.pl.rank_genes_groups_tracksplot(
             </conditional>
             <section name="advanced_common">
                 <param name="show_log" value="true"/>
+                <param name="output_anndata" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -1796,6 +1802,11 @@ sc.pl.rank_genes_groups_tracksplot(
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
+            <output name="anndata_out">
+                <assert_contents>
+                    <has_h5_keys keys="uns/paul15_clusters_colors"/>
+                </assert_contents>
+            </output>
         </test>
 
         <!-- test 24 -->
@@ -1949,6 +1960,9 @@ sc.pl.rank_genes_groups_tracksplot(
                 <param name="fontsize" value="1"/>
                 <param name="edge_width_scale" value="5"/>
             </conditional>
+            <section name="advanced_common">
+                <param name="output_anndata" value="true"/>
+            </section>
             <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
             <output name="anndata_out" ftype="h5ad">
                 <assert_contents>