# HG changeset patch
# User ebi-gxa
# Date 1620216792 0
# Node ID 59d3ce1cfaa82a42de062a1c4789d104bebd57de
# Parent  1ad1d9713563a23fba07e99e81ae40458b5d3ce4
"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 1ad1d9713563 -r 59d3ce1cfaa8 scanpy-regress-variable.xml
--- a/scanpy-regress-variable.xml	Mon Apr 12 14:45:25 2021 +0000
+++ b/scanpy-regress-variable.xml	Wed May 05 12:13:12 2021 +0000
@@ -10,6 +10,7 @@
   ln -s '${input_obj_file}' input.h5 &&
   PYTHONIOENCODING=utf-8 scanpy-regress
       --keys '${variable_keys}'
+      @SAVE_MATRIX_OPTS@
       @INPUT_OPTS@
       @OUTPUT_OPTS@
 #else
@@ -25,6 +26,7 @@
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
+    <expand macro="save_matrix_params"/>
   </inputs>
 
   <outputs>
diff -r 1ad1d9713563 -r 59d3ce1cfaa8 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Apr 12 14:45:25 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:13:12 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'"/>