# HG changeset patch
# User ebi-gxa
# Date 1572007505 14400
# Node ID e6d99b0652ec23321d42ec98ffab69b439900c5c
# Parent  6b24ebf5b7fbc3140a5b286c4ace6bdb0c50f854
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07

diff -r 6b24ebf5b7fb -r e6d99b0652ec scmap_index_cluster.xml
--- a/scmap_index_cluster.xml	Mon Sep 16 09:56:06 2019 -0400
+++ b/scmap_index_cluster.xml	Fri Oct 25 08:45:05 2019 -0400
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-index-cluster.R --input-object-file '$input_single_cell_experiment' --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cluster.R --input-object-file "preprocessed_${input_single_cell_experiment}" --cluster-col '$cluster_col' --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 as produced by 'scmap select features'" />
diff -r 6b24ebf5b7fb -r e6d99b0652ec scmap_macros.xml
--- a/scmap_macros.xml	Mon Sep 16 09:56:06 2019 -0400
+++ b/scmap_macros.xml	Fri Oct 25 08:45:05 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>