| Previous changeset 4:ba5e9bd05d5b (2022-10-18) Next changeset 6:ff2455f76a26 (2023-04-27) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2 |
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modified:
macros.xml matchms_similarity.xml |
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added:
test-data/scores.json |
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| diff -r ba5e9bd05d5b -r 28f7f2e60331 macros.xml --- a/macros.xml Tue Oct 18 11:00:55 2022 +0000 +++ b/macros.xml Tue Oct 18 13:21:54 2022 +0000 |
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| @@ -3,6 +3,7 @@ <xml name="creator"> <creator> + <yield/> <person givenName="Helge" familyName="Hecht" @@ -44,7 +45,23 @@ The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. ]]> </token> + + <token name="@HELP_matchms_networking@"> + <![CDATA[ + Documentation + For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst + and https://matchms.readthedocs.io/en/latest/. + + **Upstream Tools** + matchMS similarity + + **Downstream Tools** + + The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). + ]]> + </token> + <token name="@HELP_formatter@"> <![CDATA[ Usage @@ -66,4 +83,12 @@ +----------+-----------+---------+--------+ ]]> </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.7178586</citation> + <citation type="doi">10.21105/joss.02411</citation> + </citations> + </xml> + </macros> |
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| diff -r ba5e9bd05d5b -r 28f7f2e60331 matchms_similarity.xml --- a/matchms_similarity.xml Tue Oct 18 11:00:55 2022 +0000 +++ b/matchms_similarity.xml Tue Oct 18 13:21:54 2022 +0000 |
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| @@ -136,8 +136,5 @@ ]]> </help> - <citations> - <citation type="doi">10.5281/zenodo.7178586</citation> - <citation type="doi">10.21105/joss.02411</citation> - </citations> + <expand macro="citations"/> </tool> |
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| diff -r ba5e9bd05d5b -r 28f7f2e60331 test-data/scores.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores.json Tue Oct 18 13:21:54 2022 +0000 |
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| b'@@ -0,0 +1,1 @@\n+{"__Scores__": true, "similarity_function": {"__Similarity__": "CosineGreedy", "tolerance": 0.1, "mz_power": 0.0, "intensity_power": 1.0}, "is_symmetric": true, "references": [{"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "32", "compound_name": "C041", "retention_time": 122.44, "retention_index": 1079.198718, "peaks_json": [[73.0841293753643, 962537.0], [92.9922681974622, 25809589.0], [93.5236243719193, 7832508.0], [93.9918503397022, 4037554.0], [94.9892593290089, 9273560.0], [102.528897846033, 5258508.0], [103.032878700634, 5618676.0], [106.048287181011, 17919228.0], [116.082937025519, 19358163.0], [116.088997408008, 2749072817.0], [116.093789141941, 21174548.0], [117.085953932526, 5958559.0], [117.088526521735, 137197201.0], [117.09226575013, 144026411.0], [117.095343138483, 3078493.0], [118.085738968471, 93658275.0], [118.091857064635, 7792967.0], [118.095506285782, 3082221.0], [120.088840757968, 158124.0], [129.052817882804, 2757896.0], [144.047597981883, 6935455.0], [154.03180616847, 40749504.0], [155.035134922158, 4354801.0], [156.011148185837, 2560241.0], [172.042203916163, 16922092.0], [178.047197818956, 372134.0], [190.107642341182, 143044792.0], [191.109992585577, 20336483.0], [192.104283767627, 9359612.0], [204.050979060253, 4818700.0], [205.059630310281, 24572956.0], [244.042971889438, 1521120.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "19", "compound_name": "C078", "retention_time": 123.01, "retention_index": 1084.222756, "peaks_json": [[75.010394066048, 41579966.0], [76.0137882041242, 2876047.0], [76.0181929768627, 28340717.0], [77.0259504577085, 2087987.0], [78.0338979909698, 183026502.0], [78.5690293876576, 1621521.0], [78.8681599478139, 1487893.0], [79.0376938452989, 30093264.0], [79.0416552579741, 2825081311.0], [79.0447459388332, 28320503.0], [79.0501993561375, 4270687.0], [79.2157179170819, 1455165.0], [79.5185598181509, 1593839.0], [80.0386557190469, 10075569.0], [80.0450063493877, 149614748.0], [81.0483295726077, 3268158.0], [89.9974943554148, 1961794.0], [95.0365701495921, 4214292.0], [96.0443688524812, 20830699.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "12", "compound_name": "C115", "retention_time": 123.7, "retention_index": 1090.304487, "peaks_json": [[77.9912808985361, 1430046.0], [78.0150262817737, 37531039.0], [84.0934034839136, 3045143.0], [85.1012069274801, 7651144.0], [86.1044999837715, 502049.0], [127.023946499139, 21672536.0], [155.015395274682, 50181759.0], [173.025818014551, 19321056.0], [225.059247121035, 54449419.0], [240.031884101672, 47027617.0], [278.105692656594, 44448528.0], [332.077037506685, 36734393.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "20", "compound_name": "C072", "retention_time": 126.02, "retention_index": 1105.809524, "peaks_json": [[75.026123979198, 434239353.0], [76.0294479264598, 10769681.0], [79.0184721827801, 4406598.0], [79.0228409649542, 3040911.0], [86.0420715774215, 69402087.0], [93.9412902191997, 4117357.0], [95.0446916434486, 4401744.0], [95.9392474302401, 3764925.0], [120.033807681496, 1445863.0], [122.943972830176, 4871174.0], [131.088643222278, 12343251.0], [134.108939486662, 1310131.0], [137.026000929413, 1710939.0], [168.950062688366, 1235026.0], [176.091958662459, 68901069.0], [177.09146256329, 9695519.0], [184.040024671153, 13159137.0], [206.084125728074, 4028572.0], [249.138642058545, 13543889.0], [251.137167813194, 1490829.0]]}, {"ionmode": "negative", "spectrumtype": "Centroid", "num_peaks": "26", "compound_name": "C050", "retention_time": 128.53, "retention_index": 1117.761905, "peaks_json": [[72.0264235348245, 4721310.0], [75.0234110401587, 7374271.0], [75.0288404069534, 9420937.0], [86.9717728755449, 9553539.0], [88.9509947069327, 6380434.0], [97.088645546243, 920854.0], [100.00330732202, 18214503.0], [102.073359041231, 484549126.0], [103.002973695426, 21838182.0], [105.0182950443, 11385761.0], 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[0.07254436753789326, 7], [1.0, 45]]]}\n\\ No newline at end of file\n' |