Mercurial > repos > recetox > matchms_networking

comparison matchms_networking.xml @ 6:9982b85ff4e7 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:28:13 +0000
parents 8147d93d372d
children d8e937f335b8
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5:8147d93d372d 6:9982b85ff4e7
1 <tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09"> 1 <tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy2" profile="21.09">
2 <description>create similarity network graph from matchms similarity scores</description> 2 <description>create similarity network graph from matchms similarity scores</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import> 6 <import>help.xml</import>
14 14
15 <requirements> 15 <requirements>
16 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
17 </requirements> 17 </requirements>
18 18
19 <command detect_errors="aggressive"><![CDATA[
20 sh ${matchms_networking_cli}
21 ]]></command>
22
19 <environment_variables> 23 <environment_variables>
20 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> 24 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
21 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> 25 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
22 </environment_variables> 26 </environment_variables>
23
24 <command detect_errors="aggressive"><![CDATA[
25 sh ${matchms_networking_cli}
26 ]]></command>
27 27
28 <configfiles> 28 <configfiles>
29 <configfile name="matchms_networking_cli"> 29 <configfile name="matchms_networking_cli">
30 python3 ${__tool_directory__}/matchms_networking_wrapper.py \ 30 python3 ${__tool_directory__}/matchms_networking_wrapper.py \
31 --score_name '${score_layer_name}_score' \ 31 --score_name '${score_layer_name}_score' \
76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true" 76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true"
77 help="If set to No all unconnected nodes will be removed."/> 77 help="If set to No all unconnected nodes will be removed."/>
78 </inputs> 78 </inputs>
79 79
80 <outputs> 80 <outputs>
81 <data label="Similarity network of ${scores.name}" name="similarity_network_file"> 81 <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml">
82 <change_format> 82 <change_format>
83 <when input="graph_format" value="graphml" format="graphml"/> 83 <when input="graph_format" value="graphml" format="graphml"/>
84 <when input="graph_format" value="cyjs" format="cyjs"/> 84 <when input="graph_format" value="cyjs" format="cyjs"/>
85 <when input="graph_format" value="gexf" format="gexf"/> 85 <when input="graph_format" value="gexf" format="gexf"/>
86 <when input="graph_format" value="gml" format="gml"/> 86 <when input="graph_format" value="gml" format="gml"/>