Mercurial > repos > ebi-gxa > scanpy_compute_graph
changeset 14:a57b128ea4f6 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
| author | ebi-gxa |
|---|---|
| date | Tue, 29 Sep 2020 14:11:29 +0000 |
| parents | e6c989a9211c |
| children | 3cf0177ed87e |
| files | scanpy-neighbours.xml |
| diffstat | 1 files changed, 16 insertions(+), 3 deletions(-) [+] |
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--- a/scanpy-neighbours.xml Thu Sep 24 13:26:39 2020 +0000 +++ b/scanpy-neighbours.xml Tue Sep 29 14:11:29 2020 +0000 @@ -1,14 +1,15 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -#from pathlib import Path #if $settings.n_neighbors_file - #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip() + #set f = open($settings.n_neighbors_file.__str__) + #set n_neighbors = f.read().strip() + #silent f.close #elif $settings.n_neighbors #set n_neighbors = $settings.n_neighbors.__str__.strip() #end if @@ -106,6 +107,18 @@ <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="default" value="false"/> + <param name="n_neighbors_file" value="n_neighbors.txt"/> + <param name="n_pcs" value="50"/> + <param name="knn" value="true"/> + <param name="random_seed" value="0"/> + <param name="method" value="umap"/> + <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> + </test> + <test> + <param name="input_obj_file" value="run_pca.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="default" value="false"/> <param name="n_neighbors" value="15"/> <param name="n_pcs" value="50"/> <param name="knn" value="true"/>