# HG changeset patch
# User ebi-gxa
# Date 1620216705 0
# Node ID 3a4564b9d68514c449a05fa61cd458b33bc28991
# Parent  28ab1cdd0cf577cf9bc2321b7edadbcf389b60e9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"

diff -r 28ab1cdd0cf5 -r 3a4564b9d685 scanpy-normalise-data.xml
--- a/scanpy-normalise-data.xml	Mon Apr 12 14:43:58 2021 +0000
+++ b/scanpy-normalise-data.xml	Wed May 05 12:11:45 2021 +0000
@@ -21,12 +21,10 @@
         #if $settings.exclude.exclude_highly_expressed
             --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}'
         #end if
-        #if $settings.save_raw
-             --save-raw ${settings.save_raw}
-        #end if
     #end if
     @INPUT_OPTS@
     @OUTPUT_OPTS@
+    @SAVE_MATRIX_OPTS@
     @EXPORT_MTX_OPTS@
 ]]></command>
 
@@ -34,6 +32,7 @@
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
     <expand macro="export_mtx_params"/>
+    <expand macro="save_matrix_params"/>
      <conditional name="settings">
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
@@ -42,8 +41,6 @@
             label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
         <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" 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."/>
         <conditional name="exclude">
          <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False" 
              label="Exclude highly expressed genes?" help="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to the number specified by --normalize-to."/>
diff -r 28ab1cdd0cf5 -r 3a4564b9d685 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Apr 12 14:43:58 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:11:45 2021 +0000
@@ -30,6 +30,14 @@
   <token name="@INPUT_OPTS@">
     --input-format '${input_format}' input.h5
   </token>
+  <token name="@SAVE_MATRIX_OPTS@">
+    #if $save_raw
+      --save-raw
+    #end if
+    #if $save_layer
+      --save-layer ${settings.save_layer}
+    #end if
+  </token>
   <token name="@OUTPUT_OPTS@">
 #if str($output_format).startswith('anndata')
     --show-obj stdout --output-format anndata output.h5
@@ -51,7 +59,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.3.3">scanpy-scripts</requirement>
+      <requirement type="package" version="0.4.0">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -122,6 +130,13 @@
     </data>
   </xml>
 
+  <xml name="save_matrix_params">
+    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+      label="Save adata to adata.raw before processing?" />
+    <param name="save_layer" argument="--save-layer" type="text" optional="true"
+      label="Save adata.X to the specified layer before processing."/>
+  </xml>  
+
   <xml name="output_plot_params">
     <param name="fig_title" argument="--title" type="text" label="Figure title"/>
     <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>