Mercurial > repos > recetox > matchms_metadata_match
comparison macros.xml @ 1:b5b360897004 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
| author | recetox |
|---|---|
| date | Thu, 12 Oct 2023 13:26:40 +0000 |
| parents | 03bc9b7f40f6 |
| children | be20e19c57e8 |
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| 0:03bc9b7f40f6 | 1:b5b360897004 |
|---|---|
| 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" |