Mercurial > repos > recetox > matchms_networking

comparison matchms_networking.xml @ 8:0fd1e5d4ca3c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
author recetox
date Sun, 19 Nov 2023 14:40:18 +0000
parents d8e937f335b8
children bd6a398a05e9
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7:d8e937f335b8 8:0fd1e5d4ca3c
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@+galaxy1" 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>
26 </environment_variables> 26 </environment_variables>
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 '${score_layer_name}' \
32 --graph_format '$graph_format' \ 32 --graph_format '$graph_format' \
33 --identifier '$identifier_key' \ 33 --identifier '$identifier_key' \
34 --top_n '$top_n' \ 34 --top_n '$top_n' \
35 --max_links '$max_links' \ 35 --max_links '$max_links' \
36 --score_cutoff '$score_cutoff' \ 36 --score_cutoff '$score_cutoff' \
189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/> 189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/>
190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/> 190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/>
191 </assert_contents> 191 </assert_contents>
192 </output> 192 </output>
193 </test> 193 </test>
194 <test>
195 <param name="scores" value="networking/test9.json" ftype="json"/>
196 <param name="graph_format" value="graphml"/>
197 <param name="identifier_key" value="compound_name"/>
198 <param name="score_cutoff" value="0.4"/>
199 <param name="keep_unconnected_nodes" value="false"/>
200 <output name="similarity_network_file" ftype="graphml">
201 <assert_contents>
202 <is_valid_xml />
203 </assert_contents>
204 </output>
205 </test>
194 </tests> 206 </tests>
195 207
196 <help> 208 <help>
197 @HELP_matchms_networking@ 209 @HELP_matchms_networking@
198 @HELP_matchms@ 210 @HELP_matchms@