changeset 11:c646bd10dcab 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-plot-trajectory.xml	Fri Jun 05 09:06:18 2020 -0400
+++ b/scanpy-plot-trajectory.xml	Mon Sep 07 13:13:22 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell trajectories</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -46,8 +46,8 @@
     <param name="use_key" argument="--use-key" type="text" value="paga"
            label="The key in `.uns` that contains trajectory information"/>
     <param name="layout" argument="--layout" type="select" label="Layout functions">
-      <option value="fa" selected="true">ForceAtlas2</option>
-      <option value="fr">Fruchterman-Reingold</option>
+      <option value="fa">ForceAtlas2</option>
+      <option value="fr" selected="true">Fruchterman-Reingold</option>
       <option value="rt">Reingold-Tilford</option>
     </param>
     <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot"
@@ -85,7 +85,7 @@
 
   <tests>
     <test>
-      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_obj_file" value="paga.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="type" value="paga_compare"/>
       <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>

--- a/scanpy_macros2.xml	Fri Jun 05 09:06:18 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 13:13:22 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>