Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 14:a57b128ea4f6 draft

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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 c02d457c74016980672e64832e6cad31d703edcd-dirty"
author ebi-gxa
date Tue, 29 Sep 2020 14:11:29 +0000
parents e6c989a9211c
children 3cf0177ed87e
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13:e6c989a9211c 14:a57b128ea4f6
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@+galaxy1" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy2" 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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #from pathlib import Path
10 #if $settings.n_neighbors_file 9 #if $settings.n_neighbors_file
11 #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip() 10 #set f = open($settings.n_neighbors_file.__str__)
11 #set n_neighbors = f.read().strip()
12 #silent f.close
12 #elif $settings.n_neighbors 13 #elif $settings.n_neighbors
13 #set n_neighbors = $settings.n_neighbors.__str__.strip() 14 #set n_neighbors = $settings.n_neighbors.__str__.strip()
14 #end if 15 #end if
15 16
16 ln -s '${input_obj_file}' input.h5 && 17 ln -s '${input_obj_file}' input.h5 &&
104 <test> 105 <test>
105 <param name="input_obj_file" value="run_pca.h5"/> 106 <param name="input_obj_file" value="run_pca.h5"/>
106 <param name="input_format" value="anndata"/> 107 <param name="input_format" value="anndata"/>
107 <param name="output_format" value="anndata"/> 108 <param name="output_format" value="anndata"/>
108 <param name="default" value="false"/> 109 <param name="default" value="false"/>
110 <param name="n_neighbors_file" value="n_neighbors.txt"/>
111 <param name="n_pcs" value="50"/>
112 <param name="knn" value="true"/>
113 <param name="random_seed" value="0"/>
114 <param name="method" value="umap"/>
115 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
116 </test>
117 <test>
118 <param name="input_obj_file" value="run_pca.h5"/>
119 <param name="input_format" value="anndata"/>
120 <param name="output_format" value="anndata"/>
121 <param name="default" value="false"/>
109 <param name="n_neighbors" value="15"/> 122 <param name="n_neighbors" value="15"/>
110 <param name="n_pcs" value="50"/> 123 <param name="n_pcs" value="50"/>
111 <param name="knn" value="true"/> 124 <param name="knn" value="true"/>
112 <param name="random_seed" value="0"/> 125 <param name="random_seed" value="0"/>
113 <param name="method" value="umap"/> 126 <param name="method" value="umap"/>