Mercurial > repos > ebi-gxa > scanpy_integrate_combat
changeset 1:aaf4a7a3dd96 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 | Wed, 09 Sep 2020 12:57:32 +0000 |
| parents | 2472523c0c50 |
| children | ced09c5acba5 |
| files | scanpy-integrate-combat.xml |
| diffstat | 1 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/scanpy-integrate-combat.xml Mon Sep 07 13:06:34 2020 +0000 +++ b/scanpy-integrate-combat.xml Wed Sep 09 12:57:32 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>adjust expression for variables that might introduce batch effect</description> <macros> <import>scanpy_macros2.xml</import> @@ -22,8 +22,7 @@ @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> @@ -61,6 +60,12 @@ <param name="batch_key" value="louvain"/> <output name="output_h5" file="combat.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="combat_copy.h5" ftype="h5" compare="sim_size"/> + </test> </tests> <help><![CDATA[