Mercurial > repos > ebi-gxa > scmap_select_features

diff scmap_select_features.xml @ 1:953c7ff4069e 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 08:45:58 -0400
parents 22b605f49f5f
children 3e22b96ba4fb
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--- 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" />