Mercurial > repos > ebi-gxa > scanpy_find_cluster
comparison scanpy-find-cluster.xml @ 18:15e8a4c60418 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
| author | ebi-gxa |
|---|---|
| date | Wed, 30 Sep 2020 11:12:27 +0000 |
| parents | b45b85d5c7ec |
| children | b531acda966c |
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| 17:b45b85d5c7ec | 18:15e8a4c60418 |
|---|---|
| 1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
| 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> | 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> |
| 3 <description>based on community detection on KNN graph</description> | 3 <description>based on community detection on KNN graph</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 110 <param name="resolution" value="1.0"/> | 110 <param name="resolution" value="1.0"/> |
| 111 <param name="random_seed" value="0"/> | 111 <param name="random_seed" value="0"/> |
| 112 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> | 112 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> |
| 113 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> | 113 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> |
| 114 </test> | 114 </test> |
| 115 <test> | |
| 116 <param name="input_obj_file" value="compute_graph.h5"/> | |
| 117 <param name="input_format" value="anndata"/> | |
| 118 <param name="output_format" value="anndata"/> | |
| 119 <param name="output_txt" value="true"/> | |
| 120 <param name="default" value="false"/> | |
| 121 <param name="method" value="louvain"/> | |
| 122 <param name="resolution" value="1.0"/> | |
| 123 <param name="key_added" value="METHOD_RESOLUTION"/> | |
| 124 <param name="random_seed" value="0"/> | |
| 125 <output name="output_h5" file="louvain_1.0" ftype="h5" compare="sim_size"/> | |
| 126 <output name="output_txt" file="louvain_1.0.tsv" ftype="tsv"/> | |
| 127 </test> | |
| 115 </tests> | 128 </tests> |
| 116 | 129 |
| 117 <help><![CDATA[ | 130 <help><![CDATA[ |
| 118 ====================================================================== | 131 ====================================================================== |
| 119 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`) | 132 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`) |