| Previous changeset 7:11b4b9b85b9c (2020-05-04) Next changeset 9:0f5e46b0981a (2020-07-27) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 519352db368942656aa9cb994da421cddad5d746" |
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modified:
scmap_index_cell.xml |
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| diff -r 11b4b9b85b9c -r 441df83ffc7c scmap_index_cell.xml --- a/scmap_index_cell.xml Mon May 04 07:14:01 2020 -0400 +++ b/scmap_index_cell.xml Wed Jul 15 09:24:15 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description> <macros> <import>scmap_macros.xml</import> @@ -6,15 +6,22 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ 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 '$random_seed' + scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' #if $train_id --train-id '${train_id}' #end if + #if $n_chunks + --number-chunks '$n_chunks' + #end if + #if $n_clusters + --number-clusters '$n_clusters' + #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 name="n_chunks" type="integer" label="Number of chunks" optional="true" help="Number of chunks into which the expr matrix is split" /> + <param name="n_clusters" type="integer" label="Number of clusters" optional="true" 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> @@ -23,8 +30,6 @@ </outputs> <tests> <test> - <param name="n_chunks" value="50" /> - <param name="n_clusters" value="9" /> <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/> </test> |