Mercurial > repos > ebi-gxa > scanpy_run_umap
diff scanpy-run-umap.xml @ 15:135e8cacb57e draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
| author | ebi-gxa |
|---|---|
| date | Thu, 17 Sep 2020 16:30:12 +0000 |
| parents | f53bb2c1fa07 |
| children | 3a7b97ddf3ff |
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--- a/scanpy-run-umap.xml Fri Sep 11 11:07:03 2020 +0000 +++ b/scanpy-run-umap.xml Thu Sep 17 16:30:12 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>visualise cell clusters using UMAP</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,8 +8,16 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-run-umap - --neighbors-key '${use_graph}' +#set neighbors_key = $use_graph.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) +#set embeddings_tsv='embeddings.tsv' +--neighbors-key '${neighbors_key}' +#if $key_added + #if $neighbors_key + #set key_added = $key_added.replace('NEIGHBORS_KEY', $neighbors_key.__str__) + #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv" +#end if --key-added '${key_added}' +#end if #if $embeddings --export-embedding embeddings.tsv #end if @@ -30,6 +38,11 @@ #end if @INPUT_OPTS@ @OUTPUT_OPTS@ +#if $embeddings + #if $embeddings_tsv != 'embeddings.tsv' + && mv '${embeddings_tsv}' embeddings.tsv + #end if +#end if ]]></command>