Mercurial > repos > ebi-gxa > scmap_index_cell

diff scmap_index_cell.xml @ 1:17b3d7e04b3c draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
author ebi-gxa
date Fri, 25 Oct 2019 08:44:38 -0400
parents 628a433819c6
children dd2a84734b87
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--- 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'" />