Mercurial > repos > recetox > matchms_networking
comparison matchms_networking.xml @ 6:9982b85ff4e7 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author | recetox |
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date | Thu, 12 Oct 2023 13:28:13 +0000 |
parents | 8147d93d372d |
children | d8e937f335b8 |
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5:8147d93d372d | 6:9982b85ff4e7 |
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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"/> |