Mercurial > repos > ebi-gxa > scanpy_integrate_harmony
changeset 1:f1298838e93b 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 08:45:34 +0000 |
| parents | 8b3a52fbb482 |
| children | 739f68e3cbca |
| files | pbmc3k_filtered_gene_bc_matrices.tar.gz scanpy-integrate-harmony.xml |
| diffstat | 2 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/scanpy-integrate-harmony.xml Mon Sep 07 13:10:56 2020 +0000 +++ b/scanpy-integrate-harmony.xml Thu Sep 10 08:45:34 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>adjust principal components for variables that might introduce batch effect</description> <macros> <import>scanpy_macros2.xml</import> @@ -52,8 +52,7 @@ @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> @@ -117,6 +116,12 @@ <param name="batch_key" value="louvain"/> <output name="output_h5" file="harmony.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="harmony_copy.h5" ftype="h5" compare="sim_size"/> + </test> </tests> <help><![CDATA[