Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 16:087a7edb0995 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 16:07:10 +0000
parents 3cf0177ed87e
children 1dc0ea7a7e62
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15:3cf0177ed87e 16:087a7edb0995
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@+galaxy3" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy4" 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 #if $settings.n_neighbors_file
10 #set f = open($settings.n_neighbors_file.__str__)
11 #set n_neighbors = f.read().strip()
12 #silent f.close
13 #elif $settings.n_neighbors
14 #set n_neighbors = $settings.n_neighbors.__str__.strip()
15 #end if
16
17 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
18 PYTHONIOENCODING=utf-8 scanpy-neighbors 10 PYTHONIOENCODING=utf-8 scanpy-neighbors
19 #if $settings.default == "false" 11 #if $settings.default == "false"
12 #if $settings.n_neighbors_file
13 #set f = open($settings.n_neighbors_file.__str__)
14 #set n_neighbors = f.read().strip()
15 #silent f.close
16 #elif $settings.n_neighbors
17 #set n_neighbors = $settings.n_neighbors.__str__.strip()
18 #end if
19
20 #if $n_neighbors 20 #if $n_neighbors
21 --n-neighbors $n_neighbors 21 --n-neighbors $n_neighbors
22 #end if 22 #end if
23 #if $settings.key_added 23 #if $settings.key_added
24 #set key_added = $settings.key_added 24 #set key_added = $settings.key_added