Mercurial > repos > ebi-gxa > scanpy_find_cluster

comparison scanpy-find-cluster.xml @ 17:b45b85d5c7ec 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 14:07:52 +0000
parents 5e68e130fafe
children 15e8a4c60418
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16:5e68e130fafe 17:b45b85d5c7ec
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>