Mercurial > repos > ebi-gxa > scmap_index_cluster
changeset 2:63f1a27dce34 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
author | ebi-gxa |
---|---|
date | Fri, 03 Apr 2020 06:35:36 -0400 (2020-04-03) |
parents | e6d99b0652ec |
children | 9b60d5972dbd |
files | scmap_index_cluster.xml scmap_macros.xml |
diffstat | 2 files changed, 5 insertions(+), 6 deletions(-) [+] |
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--- a/scmap_index_cluster.xml Fri Oct 25 08:45:05 2019 -0400 +++ b/scmap_index_cluster.xml Fri Apr 03 06:35:36 2020 -0400 @@ -1,11 +1,11 @@ -<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> +<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>calculates centroids of each cell type and merges them into a single table</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-cluster.R --input-object-file "preprocessed_${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' + scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cluster.R --input-object-file "${input_single_cell_experiment}" --cluster-col '$cluster_col' --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 as produced by 'scmap select features'" /> @@ -18,7 +18,7 @@ <tests> <test> <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> - <output name="output_single_cell_experiment" file="index_cluster.rds"/> + <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size"/> <output name="plot" file="index_cluster.png"/> </test> </tests>
--- a/scmap_macros.xml Fri Oct 25 08:45:05 2019 -0400 +++ b/scmap_macros.xml Fri Apr 03 06:35:36 2020 -0400 @@ -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>