Mercurial > repos > ebi-gxa > scanpy_find_cluster

comparison scanpy-find-cluster.xml @ 19:b531acda966c 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 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
author ebi-gxa
date Wed, 07 Oct 2020 16:02:21 +0000
parents 15e8a4c60418
children 1e820072e8f1
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18:15e8a4c60418 19:b531acda966c
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@+galaxy3" profile="@PROFILE@"> 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy4" 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 #if $settings.resolution_file
10 #set f = open($settings.resolution_file.__str__)
11 #set resolution = f.read().strip()
12 #silent f.close
13 #elif $settings.resolution
14 #set resolution = $settings.resolution.__str__.strip()
15 #end if
16
17 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
18 PYTHONIOENCODING=utf-8 scanpy-find-cluster 10 PYTHONIOENCODING=utf-8 scanpy-find-cluster
19 ${method} 11 ${method}
20 #if $settings.default == "false" 12 #if $settings.default == "false"
13 #if $settings.resolution_file
14 #set f = open($settings.resolution_file.__str__)
15 #set resolution = f.read().strip()
16 #silent f.close
17 #elif $settings.resolution
18 #set resolution = $settings.resolution.__str__.strip()
19 #end if
20
21 --neighbors-key '${settings.neighbors_key}' 21 --neighbors-key '${settings.neighbors_key}'
22 #if $settings.key_added 22 #if $settings.key_added
23 #set key_added = $settings.key_added.replace('METHOD', $method.__str__) 23 #set key_added = $settings.key_added.replace('METHOD', $method.__str__)
24 #if $resolution 24 #if $resolution
25 #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__) 25 #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__)