diff scanpy-run-tsne.xml @ 12:dccd544c21ca 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-tsne.xml	Fri Jun 05 09:12:01 2020 -0400
+++ b/scanpy-run-tsne.xml	Mon Sep 07 14:01:11 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell clusters using tSNE</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -15,7 +15,7 @@
     --key-added '${key_added}'
 #end if
 #if $embeddings
-    --export-embedding embeddings.csv
+    --export-embedding embeddings.tsv
 #end if
 #if $settings.default == "false"
     #if $settings.perplexity_file
@@ -46,7 +46,7 @@
   <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="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
 
     <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation">
       <option value="X_pca">X_pca, use PCs</option>
@@ -75,7 +75,7 @@
 
   <outputs>
     <expand macro="output_data_obj" description="tSNE object"/>
-    <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings">
+    <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: tSNE embeddings">
       <filter>embeddings</filter>
     </data>
   </outputs>
@@ -89,9 +89,9 @@
       <param name="embeddings" value="true"/>
       <param name="random_seed" value="0"/>
       <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
-      <output name="output_embed" file="run_tsne.embeddings.csv" ftype="csv" compare="sim_size">
+      <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
         <assert_contents>
-          <has_n_columns n="2" sep=","/>
+          <has_n_columns n="3"/>
         </assert_contents>
       </output>
     </test>