diff scanpy-run-tsne.xml @ 5:4ed72fb8eaf8 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

--- a/scanpy-run-tsne.xml	Wed Nov 20 05:16:53 2019 -0500
+++ b/scanpy-run-tsne.xml	Mon Nov 25 14:39:34 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy6">
   <description>visualise cell clusters using tSNE</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -64,7 +64,7 @@
         <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/>
         <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/>
         <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/>
-        <param name="fast_tsne" type="boolean" checked="true" label="Use multicoreTSNE"/>
+        <param name="fast_tsne" type="boolean" checked="false" label="Use multicoreTSNE" help="Depending on the setup and version, the availability of the needed library might vary and hence fail."/>
         <param name="n_job" argument="--n-jobs" type="integer" optional="true" label="The number of jobs"/>
         <param name="n_pc" argument="--n-pcs" type="integer" optional="true" label="The number of PCs to use"/>
         <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
@@ -74,7 +74,7 @@
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: tSNE object"/>
+    <expand macro="output_data_obj" description="tSNE object"/>
     <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings">
       <filter>embeddings</filter>
     </data>