Mercurial > repos > ebi-gxa > scanpy_run_tsne

diff scanpy-run-tsne.xml @ 29:abdb61e4afa3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:06 +0000
parents 64cd33540fee
children
line wrap: on
line diff
--- a/scanpy-run-tsne.xml	Fri Oct 13 14:09:02 2023 +0000
+++ b/scanpy-run-tsne.xml	Tue Feb 27 16:43:06 2024 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy93" 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>
@@ -100,8 +100,12 @@
       <param name="perplexity_file" value="perplexity.txt"/>
       <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.tsv" ftype="tabular" compare="sim_size">
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="obsm/X_tsne"/>
+        </assert_contents>
+      </output>
+      <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1">
         <assert_contents>
           <has_n_columns n="3"/>
         </assert_contents>
@@ -115,8 +119,12 @@
       <param name="perplexity" value="30"/>
       <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.tsv" ftype="tabular" compare="sim_size">
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="obsm/X_tsne"/>
+        </assert_contents>
+      </output>
+      <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1">
         <assert_contents>
           <has_n_columns n="3"/>
         </assert_contents>