Mercurial > repos > ebi-gxa > scanpy_integrate_mnn
changeset 1:7ae183da3f07 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
| author | ebi-gxa |
|---|---|
| date | Thu, 10 Sep 2020 08:45:10 +0000 |
| parents | 873449082a29 |
| children | dc7fa97154f1 |
| files | pbmc3k_filtered_gene_bc_matrices.tar.gz scanpy-integrate-mnn.xml |
| diffstat | 2 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/scanpy-integrate-mnn.xml Mon Sep 07 13:10:40 2020 +0000 +++ b/scanpy-integrate-mnn.xml Thu Sep 10 08:45:10 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>correct batch effects by matching mutual nearest neighbors</description> <macros> <import>scanpy_macros2.xml</import> @@ -46,8 +46,7 @@ @INPUT_OPTS@ @OUTPUT_OPTS@ #else - echo "No batch variables passed, simply passing original input as output unchanged."; - cp '${input_obj_file}' '${output_h5}' + echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5 #end if ]]></command> @@ -103,6 +102,12 @@ <param name="batch_key" value="louvain"/> <output name="output_h5" file="mnn.h5" ftype="h5" compare="sim_size"/> </test> + <test> + <param name="input_obj_file" value="find_cluster.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <output name="output_h5" file="mnn_copy.h5" ftype="h5" compare="sim_size"/> + </test> </tests> <help><![CDATA[