Mercurial > repos > recetox > matchms_formatter

comparison macros.xml @ 10:1b09315a3f87 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:59 +0000
parents e1ee139b279a
children ae45992f969e
comparison
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9:715fe77be601 10:1b09315a3f87
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.17.0</token> 2 <token name="@TOOL_VERSION@">0.20.0</token>
3 3
4 <xml name="creator"> 4 <xml name="creator">
5 <creator> 5 <creator>
6 <yield/> 6 <yield/>
7 <person 7 <person
29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" 29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
30 name="RECETOX MUNI" /> 30 name="RECETOX MUNI" />
31 </creator> 31 </creator>
32 </xml> 32 </xml>
33 33
34 <token name="@HELP_matchms@"> 34 <xml name="bio.tools">
35 <![CDATA[ 35 <xrefs>
36 Documentation 36 <xref type="bio.tools">matchms</xref>
37 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst 37 </xrefs>
38 and https://matchms.readthedocs.io/en/latest/. 38 </xml>
39 39
40 Upstream Tools 40 <xml name="similarity_metrics">
41 +-----------+---------------+--------+-----------+ 41 <option value="CosineGreedy" selected="true">CosineGreedy</option>
42 | Name | Output File | Format | Parameter | 42 <option value="CosineHungarian">CosineHungarian</option>
43 +===========+===============+========+===========+ 43 <option value="ModifiedCosine">ModifiedCosine</option>
44 | RAMClustR | Mass spectra | msp | references| 44 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
45 +-----------+---------------+--------+-----------+ 45 </xml>
46 | RAMClustR | Mass spectra | msp | queries |
47 +-----------+---------------+--------+-----------+
48 46
49 Downstream Tools 47 <xml name="similarity_algorithm_params">
50 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. 48 <section name="algorithm" title="Algorithm Parameters" expanded="true">
51 ]]> 49 <param label="tolerance [Da]" name="tolerance" type="float" value="0.1"
52 </token> 50 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
53 51 <param label="mz_power" name="mz_power" type="float" value="0.0"
54 <token name="@HELP_matchms_networking@"> 52 help="The power to raise mz to in the cosine function."/>
55 <![CDATA[ 53 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
56 Documentation 54 help="The power to raise intensity to in the cosine function."/>
57 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst 55 </section>
58 and https://matchms.readthedocs.io/en/latest/. 56 </xml>
59
60 **Upstream Tools**
61 57
62 matchMS similarity 58 <xml name="input_param">
63 59 <conditional name="scores">
64 **Downstream Tools** 60 <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
65 61 checked="false"/>
66 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). 62 <when value="TRUE">
67 ]]> 63 <param label="Scores object" name="scores_in" type="data" format="json"
68 </token> 64 help="Scores objects calculated previously using one of the matchms similarity tools." />
69 65 <param label="join type" name="join_type" type="select" display="radio"
70 <token name="@HELP_formatter@"> 66 help="The join type to use for appending scores - see [1] for details.">
71 <![CDATA[ 67 <option value="left" selected="true">left</option>
72 Usage 68 <option value="inner">inner</option>
73 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**. 69 <option value="right">right</option>
74 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. 70 <option value="outer">outer</option>
71 </param>
72 </when>
73 <when value="FALSE">
74 <param label="Queries spectra" name="queries" type="data" format="msp"
75 help="Query mass spectra to match against references."/>
76 <param label="Reference spectra" name="references" type="data" format="msp"
77 help="Reference mass spectra to match against as library."/>
78 </when>
79 </conditional>
80 </xml>
75 81
76 Input Table Format 82 <xml name="citations">
77 The tool expects a JSON file containing serialized matchMS Scores object. 83 <citations>
84 <citation type="doi">10.5281/zenodo.7178586</citation>
85 <citation type="doi">10.21105/joss.02411</citation>
86 </citations>
87 </xml>
78 88
79 Output Table Format 89 <token name="@init_scores@">
80 +----------+-----------+---------+--------+ 90 from matchms.importing import load_from_msp, scores_from_json
81 | query | reference | matches | scores | 91 from matchms import Scores
82 +==========+===========+=========+========+ 92 #if $scores.use_scores
83 | C001 | Glycine | 6 | 0.5 | 93 scores = scores_from_json("$scores_in")
84 +----------+-----------+---------+--------+ 94 join_type = "$scores.join_type"
85 | C002 | Glycine | 3 | 0.34 | 95 #else
86 +----------+-----------+---------+--------+ 96 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
87 | ... | ... | ... | ... | 97 join_type = "left"
88 +----------+-----------+---------+--------+ 98 #end if
89 ]]> 99 </token>
90 </token>
91
92 <xml name="citations">
93 <citations>
94 <citation type="doi">10.5281/zenodo.7178586</citation>
95 <citation type="doi">10.21105/joss.02411</citation>
96 </citations>
97 </xml>
98 100
101 <token name="@init_logger@">
102 from matchms import set_matchms_logger_level
103 set_matchms_logger_level("WARNING")
104 </token>
99 </macros> 105 </macros>