annotate matchms_networking.xml @ 14:9f2e7e1600c0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
author recetox
date Thu, 14 Dec 2023 13:47:05 +0000
parents 3289420aaaca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
bd6a398a05e9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 0f836e483fe3727580d6d1239135203b20812504
recetox
parents: 8
diff changeset
1 <tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
2 <description>create similarity network graph from matchms similarity scores</description>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
3
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
4 <macros>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
5 <import>macros.xml</import>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
6 <import>help.xml</import>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
7 </macros>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
8 <expand macro="creator"/>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
9 <edam_operations>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
10 <edam_operation>operation_3927</edam_operation>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
11 <edam_operation>operation_3925</edam_operation>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
12 </edam_operations>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
13 <expand macro="bio.tools"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
14
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
15 <requirements>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
16 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
17 </requirements>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
18
6
9982b85ff4e7 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
19 <command detect_errors="aggressive"><![CDATA[
9982b85ff4e7 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
20 sh ${matchms_networking_cli}
9982b85ff4e7 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
21 ]]></command>
9982b85ff4e7 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
22
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
23 <environment_variables>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
24 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
25 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
26 </environment_variables>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
27
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
28 <configfiles>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
29 <configfile name="matchms_networking_cli">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
30 python3 ${__tool_directory__}/matchms_networking_wrapper.py \
8
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
31 --score_name '${score_layer_name}' \
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
32 --graph_format '$graph_format' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
33 --identifier '$identifier_key' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
34 --top_n '$top_n' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
35 --max_links '$max_links' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
36 --score_cutoff '$score_cutoff' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
37 --link_method '$link_method' \
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
38 #if $keep_unconnected_nodes
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
39 --keep_unconnected_nodes \
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
40 #end if
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
41 '$scores' \
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
42 '$similarity_network_file'
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
43 </configfile>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
44 </configfiles>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
45
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
46 <inputs>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
47 <param label="Similarity scores" name="scores" type="data" format="json"
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
48 help="matchms similarity-scores file."/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
49 <param label="Score Layer" name="score_layer_name" type="select" help="Metric of the score layer to create a network from.">
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
50 <expand macro="similarity_metrics"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
51 </param>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
52 <param label="Identifier key" name="identifier_key" type="text" value="compound_name"
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
53 help="Unique metadata identifier of each spectrum from which scores are computed."/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
54 <param label="Network-graph format" name="graph_format" type="select"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
55 help="Output format of the similarity network.">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
56 <option value="graphml">graphml</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
57 <option value="cyjs">cyjs</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
58 <option value="gexf">gexf</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
59 <option value="gml">gml</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
60 <option value="json">json</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
61 </param>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
62 <param label="Number of top edges to keep" name="top_n" type="integer" value="20"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
63 help="The number of highest-score edges to keep between a pair of nodes. Depending on 'Link method' parameter the top N edges will be selected either from disjoined
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
64 sets of individual specta or joined subset of scores between the given pair of spectra. This value has to be higher than the 'Maximum number of links'."/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
65 <param label="Maximum number of links per node" name="max_links" type="integer" value="10"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
66 help="Maximum number of links to add per node."/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
67 <param label="Score cutoff" name="score_cutoff" type="float" value="0.7" min="0.0" max="1.0"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
68 help="Minimum similarity score value to link two spectra."/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
69 <param label="Link method" name="link_method" type="select" display="radio"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
70 help="Method for computing top N edges for each node.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
71 If selected 'Single', top N nodes will be selected from disjoined sets of highest scores for nodes of a given pair (i.e., if a given edge belongs to top N scores of at least one node, it is kept).
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
72 If selected 'Mutual', top N nodes will be selected from a joined subset of a given spectra pair (i.e., if and only if a given edge belongs to top N scores of both nodes, it is kept).">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
73 <option value="single" selected="true">Single</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
74 <option value="mutual">Mutual</option>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
75 </param>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
76 <param label="Keep unconnected nodes" name="keep_unconnected_nodes" type="boolean" checked="true"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
77 help="If set to No all unconnected nodes will be removed."/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
78 </inputs>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
79
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
80 <outputs>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
81 <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
82 <change_format>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
83 <when input="graph_format" value="graphml" format="xml"/>
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
84 <when input="graph_format" value="cyjs" format="json"/>
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
85 <when input="graph_format" value="gexf" format="xml"/>
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
86 <when input="graph_format" value="gml" format="xml"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
87 <when input="graph_format" value="json" format="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
88 </change_format>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
89 </data>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
90 </outputs>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
91
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
92 <tests>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
93 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
94 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
95 <param name="graph_format" value="graphml"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
96 <param name="identifier_key" value="compound_name"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
97 <output name="similarity_network_file" ftype="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
98 <assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
99 <is_valid_xml />
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
100 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="51"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
101 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
102 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
103 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
104 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
105 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
106 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
107 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
108 <param name="graph_format" value="cyjs"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
109 <param name="identifier_key" value="compound_name"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
110 <output name="similarity_network_file" ftype="json">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
111 <assert_contents>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
112 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="51"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
113 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
114 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
115 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
116 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
117 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
118 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
119 <param name="graph_format" value="gexf"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
120 <param name="identifier_key" value="compound_name"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
121 <output name="similarity_network_file" ftype="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
122 <assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
123 <is_valid_xml />
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
124 <has_line_matching expression='.*node id="C[0-9]*" label="C[0-9]*" \/.' n="51"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
125 <has_line_matching expression='\s*.edge source="C[0-9]*" target="C[0-9]*" id="[0-9]*" weight="0.[0-9]*" \/.' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
126 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
127 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
128 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
129 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
130 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
131 <param name="graph_format" value="gml"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
132 <param name="identifier_key" value="compound_name"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
133 <output name="similarity_network_file" ftype="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
134 <assert_contents>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
135 <has_line_matching expression='\s*node \[\n\s*id [0-9]*\n\s*label "C[0-9]*"\n\s*\]' n="51"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
136 <has_line_matching expression='\s*edge \[\n\s*source [0-9]*\n\s*target [0-9]*\n\s*weight 0\.[0-9]*\n\s*\]' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
137 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
138 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
139 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
140 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
141 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
142 <param name="graph_format" value="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
143 <param name="identifier_key" value="compound_name"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
144 <output name="similarity_network_file" ftype="json">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
145 <assert_contents>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
146 <has_text_matching expression='{"id": "C[0-9]*"}' n="51"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
147 <has_text_matching expression='{"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
148 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
149 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
150 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
151 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
152 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
153 <param name="graph_format" value="graphml"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
154 <param name="identifier_key" value="compound_name"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
155 <param name="keep_unconnected_nodes" value="false"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
156 <output name="similarity_network_file" ftype="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
157 <assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
158 <is_valid_xml />
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
159 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="8"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
160 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="4"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
161 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="4"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
162 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
163 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
164 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
165 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
166 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
167 <param name="graph_format" value="graphml"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
168 <param name="identifier_key" value="compound_name"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
169 <param name="score_cutoff" value="0.4"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
170 <param name="keep_unconnected_nodes" value="false"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
171 <output name="similarity_network_file" ftype="xml">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
172 <assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
173 <is_valid_xml />
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
174 <has_line_matching expression='.*node id="C[0-9]*"\/.' n="20"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
175 <has_line_matching expression='.*edge source="C[0-9]*" target="C[0-9]*".' n="13"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
176 <has_line_matching expression='\s*.data key="d0".0\.[0-9]*.*' n="13"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
177 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
178 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
179 </test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
180 <test>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
181 <param name="scores" value="scores.json" ftype="json"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
182 <param name="graph_format" value="cyjs"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
183 <param name="identifier_key" value="compound_name"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
184 <param name="score_cutoff" value="0.8"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
185 <param name="link_method" value="mutual"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
186 <param name="keep_unconnected_nodes" value="false"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
187 <output name="similarity_network_file" ftype="json">
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
188 <assert_contents>
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
189 <has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/>
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
190 <has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
191 </assert_contents>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
192 </output>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
193 </test>
8
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
194 <test>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
195 <param name="scores" value="networking/test9.json" ftype="json"/>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
196 <param name="graph_format" value="graphml"/>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
197 <param name="identifier_key" value="compound_name"/>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
198 <param name="score_cutoff" value="0.4"/>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
199 <param name="keep_unconnected_nodes" value="false"/>
11
3289420aaaca planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 12f8b6dfa35742cdaf9904b813157a01f88ad30a
recetox
parents: 9
diff changeset
200 <output name="similarity_network_file" ftype="xml">
8
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
201 <assert_contents>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
202 <is_valid_xml />
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
203 </assert_contents>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
204 </output>
0fd1e5d4ca3c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
parents: 7
diff changeset
205 </test>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
206 </tests>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
207
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
208 <help>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
209 @HELP_matchms_networking@
5
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
210 @HELP_matchms@
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 0
diff changeset
211 </help>
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
212
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
213 <expand macro="citations"/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
214
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
215 </tool>