# HG changeset patch
# User ebi-gxa
# Date 1620216740 0
# Node ID 9fafbfcdee0d09d6e8066796d827a9658567456b
# Parent  7c601934578ba0baeb2cfa0ec28cc0c667b36f75
"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 7c601934578b -r 9fafbfcdee0d scanpy-plot-embedding.xml
--- a/scanpy-plot-embedding.xml	Mon Apr 12 14:44:32 2021 +0000
+++ b/scanpy-plot-embedding.xml	Wed May 05 12:12:20 2021 +0000
@@ -89,6 +89,7 @@
       <param name="input_format" value="anndata"/>
       <param name="basis" value="X_pca"/>
       <param name="color_by" value="louvain"/>
+      <param name="use_raw" value="false"/>
       <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/>
     </test>
   </tests>
diff -r 7c601934578b -r 9fafbfcdee0d scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Apr 12 14:44:32 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:12:20 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'"/>