# HG changeset patch
# User ebi-gxa
# Date 1620216670 0
# Node ID 5bb009f95e03d5d0d63cf8afc4ea89b2a3afeca0
# Parent  b202e078a83f2f49bc68bd906d45508f59b9b271
"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 b202e078a83f -r 5bb009f95e03 scanpy-integrate-mnn.xml
--- a/scanpy-integrate-mnn.xml	Mon Apr 12 14:43:24 2021 +0000
+++ b/scanpy-integrate-mnn.xml	Wed May 05 12:11:10 2021 +0000
@@ -42,6 +42,7 @@
         --svd-mode '${settings.svd_mode}'
     #end if
   #end if
+  @SAVE_MATRIX_OPTS@
 #end if
   @INPUT_OPTS@
   @OUTPUT_OPTS@
@@ -53,6 +54,7 @@
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
+    <expand macro="save_matrix_params"/>
     <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches.">
       <sanitizer>
         <valid initial="string.printable"/>
diff -r b202e078a83f -r 5bb009f95e03 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Apr 12 14:43:24 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:11:10 2021 +0000
@@ -30,6 +30,14 @@
   <token name="@INPUT_OPTS@">
     --input-format '${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'"/>