# HG changeset patch
# User ebi-gxa
# Date 1572007558 14400
# Node ID 953c7ff4069eb0969b8e638c596e4ba6b0010145
# Parent  22b605f49f5fde28052abdc300f31f776007daa5
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07

diff -r 22b605f49f5f -r 953c7ff4069e scmap_macros.xml
--- a/scmap_macros.xml	Mon Sep 16 09:57:48 2019 -0400
+++ b/scmap_macros.xml	Fri Oct 25 08:45:58 2019 -0400
@@ -3,7 +3,9 @@
     <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.2">scmap-cli</requirement>
+        <requirement type="package">openblas</requirement>
+        <requirement type="package">bioconductor-delayedarray</requirement>
+        <requirement type="package" version="0.0.4">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
diff -r 22b605f49f5f -r 953c7ff4069e scmap_select_features.xml
--- a/scmap_select_features.xml	Mon Sep 16 09:57:48 2019 -0400
+++ b/scmap_select_features.xml	Fri Oct 25 08:45:58 2019 -0400
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-select-features.R --input-object-file '$input_single_cell_experiment' --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-select-features.R --input-object-file "${input_single_cell_experiment}.preprocessed" --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
     ]]></command>
     <inputs>
         <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />