Mercurial > repos > ebi-gxa > scmap_select_features

diff scmap_select_features.xml @ 9:91f29745bda6 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author ebi-gxa
date Tue, 23 Apr 2024 07:48:52 +0000
parents e5aaa5bea06a
children
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--- a/scmap_select_features.xml	Fri Nov 27 13:44:55 2020 +0000
+++ b/scmap_select_features.xml	Tue Apr 23 07:48:52 2024 +0000
@@ -5,7 +5,14 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        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'
+        scmap-preprocess-sce.R 
+         --input-object "${input_single_cell_experiment}"
+         --output-sce-object "result.preprocessed" && 
+        scmap-select-features.R 
+         --input-object-file "result.preprocessed"
+         --n-features '$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" />