# HG changeset patch
# User ebi-gxa
# Date 1591210464 0
# Node ID 27d964d6264ce4fe544bc9d3484eaaef224593df
# Parent  84095a7b9867b10210d754fcffba03041fd0b956
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b28c91675a0a90e45c65f275fc2fd596b431aa45"

diff -r 84095a7b9867 -r 27d964d6264c monocle3-macros.xml
--- a/monocle3-macros.xml	Thu May 14 21:16:15 2020 +0000
+++ b/monocle3-macros.xml	Wed Jun 03 18:54:24 2020 +0000
@@ -4,6 +4,8 @@
   <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+0.1.5+galaxy1: Updated to monocle3-cli 0.0.9 for plot cells to allow for multiple genes plotting.
+
 0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).
 
 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.
diff -r 84095a7b9867 -r 27d964d6264c monocle3-plotCells.xml
--- a/monocle3-plotCells.xml	Thu May 14 21:16:15 2020 +0000
+++ b/monocle3-plotCells.xml	Wed Jun 03 18:54:24 2020 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy0" profile="@PROFILE@">
+<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy1" profile="@PROFILE@">
   <description> in the reduced dimensionality space</description>
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
   <requirements>
-    <requirement type="package" version="0.0.8">monocle3-cli</requirement>
+    <requirement type="package" version="0.0.9">monocle3-cli</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 plotCells
@@ -65,7 +65,7 @@
       <option value="LSI">LSI</option>
     </param>
     <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/>
-    <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/>
+    <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot." help="For adding more than one gene, write them as a comma separated list, with no spaces in the middle, like `crp1,crp2,cycX`."/>
     <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
       <option value="log" selected="true">Size factor correction and log transformation</option>
       <option value="size_only">Size factor correction only</option>