Mercurial > repos > ebi-gxa > scanpy_find_cluster

comparison scanpy-find-cluster.xml @ 13:c46750e2e4a4 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:06:07 +0000
parents 5a62843a2b9f
children 5e68e130fafe
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12:b456d129066d 13:c46750e2e4a4
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@+galaxy11" profile="@PROFILE@"> 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" 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 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-find-cluster 10 PYTHONIOENCODING=utf-8 scanpy-find-cluster
11 ${method} 11 ${method}
12 #if $settings.default == "false" 12 #if $settings.default == "false"
13 --use-graph '${settings.use_graph}' 13 --neighbors-key '${settings.neighbors_key}'
14 #if $settings.layer
15 --layer '${settings.layer}'
16 #end if
14 #if $settings.key_added 17 #if $settings.key_added
15 --key-added '${settings.key_added}' 18 --key-added '${settings.key_added}'
16 #end if 19 #end if
17 #if $settings.resolution_file 20 #if $settings.resolution_file
18 --resolution \$( cat $settings.resolution_file ) 21 --resolution \$( cat $settings.resolution_file )
47 50
48 <conditional name="settings"> 51 <conditional name="settings">
49 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 52 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
50 <when value="true"/> 53 <when value="true"/>
51 <when value="false"> 54 <when value="false">
52 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" 55 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
53 label="Name of the slot that holds the KNN graph"/> 56 label="Name of the slot that holds the KNN graph"/>
57 <param name="layer" argument="--layer" value="" type="text"
58 label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/>
54 <param name="key_added" argument="--key-added" type="text" optional="true" 59 <param name="key_added" argument="--key-added" type="text" optional="true"
55 label="Additional suffix to the name of the slot to save the calculated clustering"/> 60 label="Additional suffix to the name of the slot to save the calculated clustering"/>
56 61
57 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" 62 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
58 label="Resolution, high value for more and smaller clusters"/> 63 label="Resolution, high value for more and smaller clusters"/>