# HG changeset patch
# User ebi-gxa
# Date 1620216526 0
# Node ID 7fd39eb52f3869f7468ca874286547c4e46651d1
# Parent  df56c78c5a8e8e116fd75d24d115700ab670a923
"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 df56c78c5a8e -r 7fd39eb52f38 scanpy-filter-cells.xml
--- a/scanpy-filter-cells.xml	Mon Apr 12 14:40:40 2021 +0000
+++ b/scanpy-filter-cells.xml	Wed May 05 12:08:46 2021 +0000
@@ -30,6 +30,7 @@
     #set subs = ' '.join(["--subset 'c:{name}' '{subset}'".format(**$s) for $s in $subsets])
     ${subs}
 #end if
+    @SAVE_MATRIX_OPTS@
     @INPUT_OPTS@
     @OUTPUT_OPTS@
     @EXPORT_MTX_OPTS@
@@ -63,6 +64,7 @@
       <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
     </repeat>
     <param name="force_recalc" label="Force recalculation of QC vars" type="boolean" truevalue="--force-recalc" falsevalue="" help="If set, it will recalculate pcts and other existing QC vars, overwriting existing ones."/>
+    <expand macro="save_matrix_params"/>
     <expand macro="export_mtx_params"/>
   </inputs>
 
diff -r df56c78c5a8e -r 7fd39eb52f38 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Mon Apr 12 14:40:40 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:08:46 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'"/>