Mercurial > repos > ebi-gxa > scmap_index_cell
changeset 1:17b3d7e04b3c draft
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 |
| files | scmap_index_cell.xml scmap_macros.xml |
| diffstat | 2 files changed, 4 insertions(+), 2 deletions(-) [+] |
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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'" />
--- 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>