# HG changeset patch
# User ebi-gxa
# Date 1572007478 14400
# Node ID 17b3d7e04b3c096a341be4f319e2bc1852f9e51f
# Parent  628a433819c693eec50f67a0039a6f21e1a3af84
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07

diff -r 628a433819c6 -r 17b3d7e04b3c scmap_index_cell.xml
--- a/scmap_index_cell.xml	Mon Sep 16 09:55:16 2019 -0400
+++ b/scmap_index_cell.xml	Fri Oct 25 08:44:38 2019 -0400
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-index-cell.R --input-object-file '$input_single_cell_experiment' --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cell.R --input-object-file "preprocessed_${input_single_cell_experiment}" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
     ]]></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 628a433819c6 -r 17b3d7e04b3c scmap_macros.xml
--- a/scmap_macros.xml	Mon Sep 16 09:55:16 2019 -0400
+++ b/scmap_macros.xml	Fri Oct 25 08:44:38 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>