| Previous changeset 2:dd2a84734b87 (2020-04-03) Next changeset 4:faa50757208d (2020-04-28) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed" |
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modified:
scmap_index_cell.xml scmap_macros.xml |
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| diff -r dd2a84734b87 -r 5593b0744de9 scmap_index_cell.xml --- a/scmap_index_cell.xml Fri Apr 03 06:36:06 2020 -0400 +++ b/scmap_index_cell.xml Fri Apr 24 11:25:51 2020 -0400 |
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| @@ -5,12 +5,17 @@ </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-index-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$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 sce_object_preprocessed.rds && + scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' + #if $train_id + --train-id '${train_id}' + #end if ]]></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'" /> <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" /> <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" /> + <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" /> <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." /> </inputs> <outputs> |
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| diff -r dd2a84734b87 -r 5593b0744de9 scmap_macros.xml --- a/scmap_macros.xml Fri Apr 03 06:36:06 2020 -0400 +++ b/scmap_macros.xml Fri Apr 24 11:25:51 2020 -0400 |
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| @@ -4,7 +4,7 @@ <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.0.5">scmap-cli</requirement> + <requirement type="package" version="0.0.8">scmap-cli</requirement> <yield/> </requirements> </xml> @@ -38,6 +38,7 @@ url = {https://github.com/ebi-gene-expression-group/scmap-cli.git}, } </citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> <yield /> </citations> </xml> |