changeset 19:cb43c5d3acd3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f

--- a/cluster_reduce_dimension.xml	Thu Sep 19 06:42:05 2024 +0000
+++ b/cluster_reduce_dimension.xml	Thu Oct 03 22:42:14 2024 +0000
@@ -224,7 +224,7 @@
 #end if
 
 @CMD_ANNDATA_WRITE_OUTPUTS@
-        ]]>     
+        ]]>
         </configfile>
     </configfiles>
     <inputs>
@@ -479,7 +479,7 @@
                 </assert_contents>
             </output>
         </test>
-        
+
         <!-- test 5 -->
         <test expect_num_outputs="2">
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
@@ -501,7 +501,7 @@
                 </assert_contents>
             </output>
         </test>
-        
+
         <!-- test 6 -->
         <test expect_num_outputs="2">
             <param name="adata" value="krumsiek11.h5ad"/>
@@ -529,7 +529,7 @@
                 </assert_contents>
             </output>
         </test>
-        
+
         <!-- test 7 -->
         <test expect_num_outputs="2">
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
@@ -581,7 +581,7 @@
             <output name="anndata_out" ftype="h5ad">
                 <assert_contents>
                     <has_h5_keys keys="uns/draw_graph"/>
-                    <has_h5_keys keys="obsm/X_draw_graph_fr"/>
+                    <has_h5_keys keys="obsm/X_draw_graph_fa"/>
                 </assert_contents>
             </output>
         </test>
@@ -615,7 +615,7 @@
         </test>
 
         <!-- test 10 -->
-        <test expect_num_outputs="2">    
+        <test expect_num_outputs="2">
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.paga"/>
@@ -665,7 +665,7 @@
         </test>
     </tests>
     <help><![CDATA[
-        
+
 Cluster cells into subgroups (`tl.louvain`)
 ===========================================
 

--- a/macros.xml	Thu Sep 19 06:42:05 2024 +0000
+++ b/macros.xml	Thu Oct 03 22:42:14 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
@@ -10,6 +10,7 @@
             <requirement type="package" version="2.2.2">pandas</requirement>
             <requirement type="package" version="1.14.1">scipy</requirement>
             <requirement type="package" version="0.14.2">statsmodels</requirement>
+            <requirement type="package" version="0.3.5">fa2</requirement>
             <yield />
         </requirements>
     </xml>
@@ -587,7 +588,7 @@
     ]]>
     </token>
     <token name="@CMD_SHOW_NONE@"><![CDATA[
-        show=None
+    show=None
         ]]>
     </token>
     <token name="@CMD_VAR_NAMES_HEADER_CHECK@"><![CDATA[
@@ -1197,14 +1198,13 @@
     </xml>
     <xml name="params_pl_paga">
         <param argument="threshold" type="float" min="0" value="" optional="true" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
-        <expand macro="param_groups"/>
+        <param argument="labels" type="text" value="" optional="true" label="The node labels" help="This defaults to the group labels stored in the categorical for which paga() has been computed">
+            <expand macro="sanitize_query"/>
+        </param>
         <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'.">
             <expand macro="sanitize_query"/>
         </param>
         <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing"/>
-        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed.">
-            <expand macro="sanitize_query"/>
-        </param>
         <expand macro="param_layout"/>
         <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout"/>
         <param argument="random_state" type="integer" value="0" label="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/>
@@ -1237,9 +1237,9 @@
         #if str($method.threshold) != '':
     threshold=$method.threshold,
         #end if
-        #if str($method.groups) != '':
-            #set $groups=([x.strip() for x in str($method.groups).split(',')])
-    groups=$groups,
+        #if str($method.labels) != '':
+            #set $labels=([x.strip() for x in str($method.labels).split(',')])
+    labels=$labels,
         #end if
         #if str($method.color) != '':
             #set $color=([x.strip() for x in str($method.color).split(',')])
@@ -1248,10 +1248,6 @@
         #if $method.pos:
     pos=np.fromfile($method.pos, dtype=dt),
         #end if
-        #if str($method.labels) != '':
-            #set $labels=([x.strip() for x in str($method.labels).split(',')])
-    labels=$labels,
-        #end if
     layout='$method.layout',
         #if $method.init_pos:
     init_pos=np.fromfile($method.init_pos, dtype=dt),
@@ -1269,7 +1265,9 @@
     dashed_edges='$method.dashed_edges',
         #end if
     single_component=$method.single_component,
+        #if str($method.fontsize) != '':
     fontsize=$method.fontsize,
+        #end if
     node_size_scale=$method.node_size_scale,
     node_size_power=$method.node_size_power,
     edge_width_scale=$method.edge_width_scale,