Mercurial > repos > ebi-gxa > scanpy_find_cluster
comparison scanpy-find-cluster.xml @ 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 |
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date | Tue, 29 Sep 2020 14:07:52 +0000 |
parents | 5e68e130fafe |
children | 15e8a4c60418 |
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16:5e68e130fafe | 17:b45b85d5c7ec |
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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@+galaxy1" profile="@PROFILE@"> | 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy2" 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"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 #from pathlib import Path | |
10 #if $settings.resolution_file | 9 #if $settings.resolution_file |
11 #set resolution = Path($settings.resolution_file.__str__).read_text().strip() | 10 #set f = open($settings.resolution_file.__str__) |
11 #set resolution = f.read().strip() | |
12 #silent f.close | |
12 #elif $settings.resolution | 13 #elif $settings.resolution |
13 #set resolution = $settings.resolution.__str__.strip() | 14 #set resolution = $settings.resolution.__str__.strip() |
14 #end if | 15 #end if |
15 | 16 |
16 ln -s '${input_obj_file}' input.h5 && | 17 ln -s '${input_obj_file}' input.h5 && |
93 <param name="input_obj_file" value="compute_graph.h5"/> | 94 <param name="input_obj_file" value="compute_graph.h5"/> |
94 <param name="input_format" value="anndata"/> | 95 <param name="input_format" value="anndata"/> |
95 <param name="output_format" value="anndata"/> | 96 <param name="output_format" value="anndata"/> |
96 <param name="output_txt" value="true"/> | 97 <param name="output_txt" value="true"/> |
97 <param name="default" value="false"/> | 98 <param name="default" value="false"/> |
99 <param name="resolution_file" value="resolution.txt"/> | |
100 <param name="random_seed" value="0"/> | |
101 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> | |
102 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> | |
103 </test> | |
104 <test> | |
105 <param name="input_obj_file" value="compute_graph.h5"/> | |
106 <param name="input_format" value="anndata"/> | |
107 <param name="output_format" value="anndata"/> | |
108 <param name="output_txt" value="true"/> | |
109 <param name="default" value="false"/> | |
98 <param name="resolution" value="1.0"/> | 110 <param name="resolution" value="1.0"/> |
99 <param name="random_seed" value="0"/> | 111 <param name="random_seed" value="0"/> |
100 <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"/> |
101 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> | 113 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> |
102 </test> | 114 </test> |