# HG changeset patch
# User ebi-gxa
# Date 1572005990 14400
# Node ID 059f8d2e8be1811110da6ecc1717211257bc7f3d
# Parent  e541f264fad2c8fecc2dd99dc860eeabf3f388ba
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d

diff -r e541f264fad2 -r 059f8d2e8be1 dataset_102795.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dataset_102795.dat	Fri Oct 25 08:19:50 2019 -0400
@@ -0,0 +1,32520 @@
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diff -r e541f264fad2 -r 059f8d2e8be1 dataset_102795.dat.zip
Binary file dataset_102795.dat.zip has changed
diff -r e541f264fad2 -r 059f8d2e8be1 input.h5
Binary file input.h5 has changed
diff -r e541f264fad2 -r 059f8d2e8be1 input.h5.zip
Binary file input.h5.zip has changed
diff -r e541f264fad2 -r 059f8d2e8be1 scanpy-normalise-data.xml
--- a/scanpy-normalise-data.xml	Mon Sep 16 08:11:56 2019 -0400
+++ b/scanpy-normalise-data.xml	Fri Oct 25 08:19:50 2019 -0400
@@ -11,6 +11,7 @@
     --normalize-to ${scale_factor}
     --fraction ${fraction}
     --save-raw ${save_raw}
+    ${log_transform}
     @INPUT_OPTS@
     @OUTPUT_OPTS@
 ]]></command>
@@ -23,6 +24,8 @@
     <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
            label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
            help="Only non-excluded genes will sum up the target number."/>
+    <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-tranform" checked="True" 
+           label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
     <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
            label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
     <expand macro="export_mtx_params"/>
diff -r e541f264fad2 -r 059f8d2e8be1 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Sep 16 08:11:56 2019 -0400
+++ b/scanpy_macros2.xml	Fri Oct 25 08:19:50 2019 -0400
@@ -1,9 +1,11 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.4.2</token>
+  <token name="@TOOL_VERSION@">1.4.3</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
+
 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
 
 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
@@ -31,7 +33,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement>
+      <requirement type="package" version="0.2.5.post1">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>