Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 30:22bd5861706d draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:03 +0000
parents f776e3ed3c03
children
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29:f776e3ed3c03 30:22bd5861706d
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive 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"/>
107 <param name="n_neighbors_file" value="n_neighbors.txt"/> 107 <param name="n_neighbors_file" value="n_neighbors.txt"/>
108 <param name="n_pcs" value="50"/> 108 <param name="n_pcs" value="50"/>
109 <param name="knn" value="true"/> 109 <param name="knn" value="true"/>
110 <param name="random_seed" value="0"/> 110 <param name="random_seed" value="0"/>
111 <param name="method" value="umap"/> 111 <param name="method" value="umap"/>
112 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> 112 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
113 </test> 113 </test>
114 <test> 114 <test>
115 <param name="input_obj_file" value="run_pca.h5"/> 115 <param name="input_obj_file" value="run_pca.h5"/>
116 <param name="input_format" value="anndata"/> 116 <param name="input_format" value="anndata"/>
117 <param name="output_format" value="anndata"/> 117 <param name="output_format" value="anndata"/>
119 <param name="n_neighbors" value="15"/> 119 <param name="n_neighbors" value="15"/>
120 <param name="n_pcs" value="50"/> 120 <param name="n_pcs" value="50"/>
121 <param name="knn" value="true"/> 121 <param name="knn" value="true"/>
122 <param name="random_seed" value="0"/> 122 <param name="random_seed" value="0"/>
123 <param name="method" value="umap"/> 123 <param name="method" value="umap"/>
124 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> 124 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
125 </test> 125 </test>
126 </tests> 126 </tests>
127 127
128 <help><![CDATA[ 128 <help><![CDATA[
129 ============================================================= 129 =============================================================