Mercurial > repos > recetox > matchms_formatter

comparison macros.xml @ 11:ae45992f969e 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 13:29:16 +0000
parents 1b09315a3f87
children 1e58bf51a0e5
comparison
equal deleted inserted replaced
10:1b09315a3f87 11:ae45992f969e
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.20.0</token> 2 <token name="@TOOL_VERSION@">0.22.0</token>
3 3
4 <xml name="creator"> 4 <xml name="creator">
5 <creator> 5 <creator>
6 <yield/> 6 <yield/>
7 <person 7 <person
55 </section> 55 </section>
56 </xml> 56 </xml>
57 57
58 <xml name="input_param"> 58 <xml name="input_param">
59 <conditional name="scores"> 59 <conditional name="scores">
60 <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE" 60 <param name="use_scores" label="Use Scores Object" type="select">
61 checked="false"/> 61 <option value="False" selected="true">FALSE</option>
62 <when value="TRUE"> 62 <option value="True">TRUE</option>
63 </param>
64 <when value="True">
63 <param label="Scores object" name="scores_in" type="data" format="json" 65 <param label="Scores object" name="scores_in" type="data" format="json"
64 help="Scores objects calculated previously using one of the matchms similarity tools." /> 66 help="Scores objects calculated previously using one of the matchms similarity tools." />
65 <param label="join type" name="join_type" type="select" display="radio" 67 <param label="join type" name="join_type" type="select" display="radio"
66 help="The join type to use for appending scores - see [1] for details."> 68 help="The join type to use for appending scores - see [1] for details.">
67 <option value="left" selected="true">left</option> 69 <option value="left" selected="true">left</option>
68 <option value="inner">inner</option> 70 <option value="inner">inner</option>
69 <option value="right">right</option> 71 <option value="right">right</option>
70 <option value="outer">outer</option> 72 <option value="outer">outer</option>
71 </param> 73 </param>
72 </when> 74 </when>
73 <when value="FALSE"> 75 <when value="False">
74 <param label="Queries spectra" name="queries" type="data" format="msp" 76 <param label="Queries spectra" name="queries" type="data" format="msp"
75 help="Query mass spectra to match against references."/> 77 help="Query mass spectra to match against references."/>
76 <param label="Reference spectra" name="references" type="data" format="msp" 78 <param label="Reference spectra" name="references" type="data" format="msp"
77 help="Reference mass spectra to match against as library."/> 79 help="Reference mass spectra to match against as library."/>
78 </when> 80 </when>
87 </xml> 89 </xml>
88 90
89 <token name="@init_scores@"> 91 <token name="@init_scores@">
90 from matchms.importing import load_from_msp, scores_from_json 92 from matchms.importing import load_from_msp, scores_from_json
91 from matchms import Scores 93 from matchms import Scores
92 #if $scores.use_scores 94 #if $scores.use_scores == "True"
93 scores = scores_from_json("$scores_in") 95 scores = scores_from_json("$scores_in")
94 join_type = "$scores.join_type" 96 join_type = "$scores.join_type"
95 #else 97 #else
96 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False) 98 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
97 join_type = "left" 99 join_type = "left"