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comparison matchms_similarity.xml @ 4:ba5e9bd05d5b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
author recetox
date Tue, 18 Oct 2022 11:00:55 +0000
parents 9f8532c99845
children 28f7f2e60331
comparison
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3:9f8532c99845 4:ba5e9bd05d5b
1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy2" python_template_version="3.8"> 1 <tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8">
2 <description>calculate the similarity score and matched peaks</description> 2 <description>calculate the similarity score and matched peaks</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
37 "$similarity_metric" \ 37 "$similarity_metric" \
38 "$algorithm.tolerance" \ 38 "$algorithm.tolerance" \
39 "$algorithm.mz_power" \ 39 "$algorithm.mz_power" \
40 "$algorithm.intensity_power" \ 40 "$algorithm.intensity_power" \
41 "$similarity_scores" \ 41 "$similarity_scores" \
42 "$similarity_matches"
43 </configfile> 42 </configfile>
44 </configfiles> 43 </configfiles>
45 44
46 <inputs> 45 <inputs>
47 <param label="Queries spectra" name="queries" type="data" format="msp,mgf" 46 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
80 </when> 79 </when>
81 </conditional> 80 </conditional>
82 </inputs> 81 </inputs>
83 82
84 <outputs> 83 <outputs>
85 <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="tsv"/> 84 <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="json"/>
86 <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="tsv"/>
87 </outputs> 85 </outputs>
88 86
89 <tests> 87 <tests>
90 <test> 88 <test> <!-- TEST #1: Test scoring of different file formats. -->
91 <param name="references" value="similarity/fill.mgf" ftype="mgf"/> 89 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
92 <param name="queries" value="similarity/fill.msp" ftype="msp"/> 90 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
93 <param name="similarity_metric" value="CosineGreedy"/> 91 <param name="similarity_metric" value="CosineGreedy"/>
94 <output name="similarity_scores" file="similarity/scores_test1_out.tsv" ftype="tsv" 92 <output name="similarity_scores" file="similarity/scores_test1_out.json" ftype="json"
95 checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/> 93 checksum="md5$72f96c48f8c34cf2a7c37d3aede33ca0"/>
96 <output name="similarity_matches" file="similarity/matches_test1_out.tsv" ftype="tsv"
97 checksum="md5$aab26ef4a0e80a53699832db72c06340"/>
98 </test> 94 </test>
99 <test> 95 <test> <!-- TEST #2: Test scoring of the same file formats. -->
100 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> 96 <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
101 <param name="queries" value="similarity/fill.msp" ftype="msp"/> 97 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
102 <param name="similarity_metric" value="CosineGreedy"/> 98 <param name="similarity_metric" value="CosineGreedy"/>
103 <output name="similarity_scores" file="scores_test2_out.tsv" ftype="tsv" 99 <output name="similarity_scores" file="similarity/scores_test2_out.json" ftype="json"
104 checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/> 100 checksum="md5$d325a895f74262087553d08cc40a99aa"/>
105 <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv"
106 checksum="md5$28dc16ce45105234437e53d59e240046"/>
107 </test> 101 </test>
108 <test> 102 <test> <!-- TEST #3: Test scoring with applying RI filtering. -->
109 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> 103 <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
110 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
111 <param name="similarity_metric" value="CosineHungarian"/>
112 <output name="similarity_scores" file="similarity/scores_test3_out.tsv" ftype="tsv"
113 checksum="md5$1341369778036e0a267ff723f8cfca9c"/>
114 <output name="similarity_matches" file="similarity/matches_test3_out.tsv" ftype="tsv"
115 checksum="md5$28dc16ce45105234437e53d59e240046"/>
116 </test>
117 <test>
118 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
119 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
120 <param name="similarity_metric" value="ModifiedCosine"/>
121 <output name="similarity_scores" file="similarity/scores_test4_out.tsv" ftype="tsv"/>
122 <output name="similarity_matches" file="similarity/matches_test4_out.tsv" ftype="tsv"/>
123 </test>
124 <test>
125 <param name="queries" value="similarity/fill.msp" ftype="msp"/>
126 <param name="similarity_metric" value="CosineHungarian"/>
127 <param name="is_symmetric" value="TRUE"/>
128 <output name="similarity_scores" file="similarity/scores_test5_out.tsv" ftype="tsv"/>
129 <output name="similarity_matches" file="similarity/matches_test5_out.tsv" ftype="tsv"/>
130 </test>
131 <test>
132 <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
133 <param name="queries" value="similarity/fill2.msp" ftype="msp"/> 104 <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
134 <conditional name="ri_filtering"> 105 <conditional name="ri_filtering">
135 <param name="is_true" value="True"></param> 106 <param name="is_true" value="True"></param>
136 <param name="tolerance" value="60.0" /> 107 <param name="tolerance" value="60.0" />
137 </conditional> 108 </conditional>
138 <param name="similarity_metric" value="CosineGreedy"/> 109 <param name="similarity_metric" value="CosineHungarian"/>
139 <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/> 110 <output name="similarity_scores" file="similarity/scores_test3_out.json" ftype="json"
140 <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/> 111 checksum="md5$437c03775ebe978f03b7c63aa09ee52e"/>
141 </test> 112 </test>
142 <test> 113 <test> <!-- TEST #4: Test symmetric scoring. -->
143 <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/> 114 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
144 <param name="queries" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/> 115 <param name="is_symmetric" value="TRUE"/>
145 <param name="similarity_metric" value="NeutralLossesCosine"/> 116 <param name="similarity_metric" value="NeutralLossesCosine"/>
146 <output name="similarity_scores" file="similarity/scores_test7_out.tsv" ftype="tsv"/> 117 <output name="similarity_scores" file="similarity/scores_test4_out.json" ftype="json"
147 <output name="similarity_matches" file="similarity/matches_test7_out.tsv" ftype="tsv"/> 118 checksum="md5$951b3bad2207d8301e0c60397533e607"/>
148 </test> 119 </test>
149 <test> 120 <test> <!-- TEST #5: Test symmetric scoring with applying RI filtering. -->
150 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> 121 <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
151 <param name="similarity_metric" value="CosineGreedy"/> 122 <param name="similarity_metric" value="ModifiedCosine"/>
152 <param name="is_symmetric" value="TRUE" /> 123 <param name="is_symmetric" value="TRUE" />
153 <conditional name="ri_filtering"> 124 <conditional name="ri_filtering">
154 <param name="is_true" value="True"></param> 125 <param name="is_true" value="True"></param>
155 <param name="tolerance" value="60.0" /> 126 <param name="tolerance" value="60.0" />
156 </conditional> 127 </conditional>
157 <output name="similarity_scores" file="similarity/scores_test8_out.tsv" ftype="tsv"/> 128 <output name="similarity_scores" file="similarity/scores_test5_out.json" ftype="json"
158 <output name="similarity_matches" file="similarity/matches_test8_out.tsv" ftype="tsv"/> 129 checksum="md5$31f83451443a1996fbd7fbc204803481"/>
159 </test> 130 </test>
160 </tests> 131 </tests>
161 132
162 <help> 133 <help>
163 <![CDATA[ 134 <![CDATA[
164 @HELP_matchms@ 135 @HELP_matchms@
165 ]]> 136 ]]>
166 </help> 137 </help>
167 138
168 <citations> 139 <citations>
169 <citation type="doi">10.5281/zenodo.4589154</citation> 140 <citation type="doi">10.5281/zenodo.7178586</citation>
170 <citation type="doi">10.21105/joss.02411</citation> 141 <citation type="doi">10.21105/joss.02411</citation>
171 </citations> 142 </citations>
172 </tool> 143 </tool>