Mercurial > repos > ebi-gxa > scanpy_run_pca

changeset 12:3e7ede8e1c94 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:14:04 +0000
parents aee7b7f9cae3
children a8f94e4a2526
files scanpy-run-pca.xml scanpy_macros2.xml
diffstat 2 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/scanpy-run-pca.xml	Fri Jun 05 09:09:03 2020 -0400
+++ b/scanpy-run-pca.xml	Mon Sep 07 13:14:04 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>for dimensionality reduction</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -56,7 +56,7 @@
 
   <outputs>
     <expand macro="output_data_obj" description="PCA object"/>
-    <data name="output_embed" format="tsv" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings">
+    <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings">
       <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter>
     </data>
   </outputs>
@@ -70,12 +70,12 @@
       <param name="n_pcs" value="50"/>
       <param name="zero_center" value="true"/>
       <param name="svd_solver" value="arpack"/>
-      <param name="random_seed" value="0"/>
+      <param name="random_seed" value="1"/>
       <param name="chunked" value="false"/>
       <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/>
-      <output name="output_embed" file="run_pca.embeddings.csv" ftype="csv" compare="sim_size">
+      <output name="output_embed" file="run_pca.embeddings.tsv" ftype="tabular" compare="sim_size" >
         <assert_contents>
-          <has_n_columns n="50" sep=","/>
+          <has_n_columns n="51"/>
         </assert_contents>
       </output>
     </test>
--- a/scanpy_macros2.xml	Fri Jun 05 09:09:03 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 13:14:04 2020 +0000
@@ -1,10 +1,13 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.4.3</token>
+  <token name="@TOOL_VERSION@">1.6.0</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
   <token name="@PROFILE@">18.01</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/
+
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
 
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
@@ -46,7 +49,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.2.10">scanpy-scripts</requirement>
+      <requirement type="package" version="0.3.0">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>