diff scanpy-run-umap.xml @ 12:f53bb2c1fa07 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-umap.xml	Fri Jun 05 09:14:06 2020 -0400
+++ b/scanpy-run-umap.xml	Mon Sep 07 14:00:37 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell clusters using UMAP</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -8,10 +8,10 @@
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-run-umap
-    --use-graph '${use_graph}'
+    --neighbors-key '${use_graph}'
     --key-added '${key_added}'
 #if $embeddings
-    --export-embedding embeddings.csv
+    --export-embedding embeddings.tsv
 #end if
 #if $settings.default == "false"
     --n-components ${settings.n_components}
@@ -36,8 +36,8 @@
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
-    <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/>
-    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+    <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
+    <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 embedding"/>
@@ -65,7 +65,7 @@
 
   <outputs>
     <expand macro="output_data_obj" description="UMAP object"/>
-    <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings">
+    <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: UMAP embeddings">
       <filter>embeddings</filter>
     </data>
   </outputs>
@@ -79,9 +79,9 @@
       <param name="embeddings" value="true"/>
       <param name="random_seed" value="0"/>
       <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/>
-      <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size">
+      <output name="output_embed" file="run_umap.embeddings.tsv" ftype="tabular" compare="sim_size">
         <assert_contents>
-          <has_n_columns n="2" sep=","/>
+          <has_n_columns n="3"/>
         </assert_contents>
       </output>
     </test>