Mercurial > repos > ebi-gxa > scanpy_find_cluster
changeset 17:b45b85d5c7ec 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 14:07:52 +0000 |
| parents | 5e68e130fafe |
| children | 15e8a4c60418 |
| files | scanpy-find-cluster.xml |
| diffstat | 1 files changed, 15 insertions(+), 3 deletions(-) [+] |
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--- a/scanpy-find-cluster.xml Thu Sep 17 16:24:22 2020 +0000 +++ b/scanpy-find-cluster.xml Tue Sep 29 14:07:52 2020 +0000 @@ -1,14 +1,15 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>based on community detection on KNN graph</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -#from pathlib import Path #if $settings.resolution_file - #set resolution = Path($settings.resolution_file.__str__).read_text().strip() + #set f = open($settings.resolution_file.__str__) + #set resolution = f.read().strip() + #silent f.close #elif $settings.resolution #set resolution = $settings.resolution.__str__.strip() #end if @@ -95,6 +96,17 @@ <param name="output_format" value="anndata"/> <param name="output_txt" value="true"/> <param name="default" value="false"/> + <param name="resolution_file" value="resolution.txt"/> + <param name="random_seed" value="0"/> + <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> + <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> + </test> + <test> + <param name="input_obj_file" value="compute_graph.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="output_txt" value="true"/> + <param name="default" value="false"/> <param name="resolution" value="1.0"/> <param name="random_seed" value="0"/> <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>