| Previous changeset 1:17b3d7e04b3c (2019-10-25) Next changeset 3:5593b0744de9 (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd" |
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modified:
scmap_index_cell.xml scmap_macros.xml |
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| diff -r 17b3d7e04b3c -r dd2a84734b87 scmap_index_cell.xml --- a/scmap_index_cell.xml Fri Oct 25 08:44:38 2019 -0400 +++ b/scmap_index_cell.xml Fri Apr 03 06:36:06 2020 -0400 |
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| @@ -1,11 +1,11 @@ -<tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> +<tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description> <macros> <import>scmap_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - 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 '$random_seed' + scmap-preprocess-sce.R --input-object "${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' ]]></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'" /> @@ -21,7 +21,7 @@ <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"/> + <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ |
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| diff -r 17b3d7e04b3c -r dd2a84734b87 scmap_macros.xml --- a/scmap_macros.xml Fri Oct 25 08:44:38 2019 -0400 +++ b/scmap_macros.xml Fri Apr 03 06:36:06 2020 -0400 |
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| @@ -1,11 +1,10 @@ <macros> <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token> + <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> - <requirement type="package">openblas</requirement> - <requirement type="package">bioconductor-delayedarray</requirement> - <requirement type="package" version="0.0.4">scmap-cli</requirement> + <requirement type="package" version="0.0.5">scmap-cli</requirement> <yield/> </requirements> </xml> |