diff scanpy-run-diffmap.xml @ 12:26e1a99e3c0f draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

--- a/scanpy-run-diffmap.xml	Fri Jun 05 09:05:00 2020 -0400
+++ b/scanpy-run-diffmap.xml	Mon Sep 07 14:02:22 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
+<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>calculate diffusion components</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -10,7 +10,7 @@
 PYTHONIOENCODING=utf-8 scanpy-cli embed diffmap
     --n-comps ${n_comps}
 #if $use_graph
-    --use-graph '${use_graph}'
+    --neighbors-key '${use_graph}'
 #end if
 #if $key_added
     --key-added '${key_added}'
@@ -29,7 +29,7 @@
     <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
            truevalue="--export-embedding embed.tsv" falsevalue=""
            label="Export embeddings as a tab-separated text table"/>
-    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+    <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
            label="Name of the slot that holds the KNN graph"/>
     <param name="key_added" argument="--key-added" type="text" optional="true"
            label="Additional suffix to the name of the slot to save the calculated diffusion map"/>
@@ -44,14 +44,14 @@
 
   <tests>
     <test>
-      <param name="input_obj_file" value="diffmap.h5"/>
+      <param name="input_obj_file" value="find_cluster.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="n_dcs" value="10"/>
-      <param name="root_attr" value="leiden"/>
+      <param name="root_attr" value="louvain"/>
       <param name="root_value" value="1"/>
       <param name="use_graph" value="neighbors"/>
-      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="diffmap.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>