Mercurial > repos > ebi-gxa > scanpy_read_10x

changeset 12:5ff50f4a26cd 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 14:02:50 +0000
parents d92e6f12b790
children 8efba12e8f58
files scanpy-read-10x.xml scanpy_macros2.xml
diffstat 2 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/scanpy-read-10x.xml	Fri Jun 05 09:13:51 2020 -0400
+++ b/scanpy-read-10x.xml	Mon Sep 07 14:02:50 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>into hdf5 object handled by scanpy</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -47,7 +47,7 @@
       <param name="barcodes" value="barcodes.tsv"/>
       <!-- <param name="cell_meta" value=""/> -->
       <param name="output_format" value="anndata"/>
-      <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5ad" file="read_10x.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>
 
--- a/scanpy_macros2.xml	Fri Jun 05 09:13:51 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 14:02:50 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>