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hechthhechth
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Merge pull request #644 from acquayefrank/issues/577-matchms
Replaced output of matchms from tsv to tabular
2 parents d6102c6 + ed43aac commit a1009ac

10 files changed

+343
-265
lines changed

‎tools/matchms/matchms_add_key.xml‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>Set metadata key in MSP to static value</description>
33

44
<macros>
@@ -67,8 +67,10 @@ save_as_msp(new_spectra, "${output}")
6767
<tests>
6868
<test>
6969
<param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
70-
<param name="key" value="tool_used"/>
71-
<param name="value" value="matchms"/>
70+
<repeat name="attribute_repeat">
71+
<param name="key" value="tool_used"/>
72+
<param name="value" value="matchms"/>
73+
</repeat>
7274
<output name="output" file="add_key/out_matchms_add_key.msp" ftype="msp"/>
7375
</test>
7476
<test>

‎tools/matchms/matchms_convert.xml‎

Lines changed: 60 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
1+
<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy1" profile="21.05">
22
<description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
33

44
<macros>
@@ -99,52 +99,75 @@ rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.t
9999
</data>
100100
</outputs>
101101

102-
<tests>
103-
<test>
104-
<param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
105-
<param name="harmonization_metadata" value="False"/>
102+
<tests>
103+
<!-- Test 1: Convert to MGF -->
104+
<test>
105+
<conditional name="output_file">
106106
<param name="output_format" value="mgf"/>
107-
<output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/>
108-
</test>
109-
<test>
110-
<param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
111-
<param name="harmonization_metadata" value="False"/>
107+
</conditional>
108+
<param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
109+
<param name="harmonization_metadata" value="False"/>
110+
<output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/>
111+
</test>
112+
113+
<!-- Test 2: Convert to JSON -->
114+
<test>
115+
<conditional name="output_file">
112116
<param name="output_format" value="json"/>
113-
<output name="converted_library" file="convert/json_out.json" ftype="json"/>
114-
</test>
115-
<test>
116-
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
117-
<param name="harmonization_metadata" value="False"/>
118-
<param name="export_peak_comments" value="False"/>
117+
</conditional>
118+
<param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
119+
<param name="harmonization_metadata" value="False"/>
120+
<output name="converted_library" file="convert/json_out.json" ftype="json"/>
121+
</test>
122+
123+
<!-- Test 3: Convert to MSP with matchms style -->
124+
<test>
125+
<conditional name="output_file">
119126
<param name="output_format" value="msp"/>
120-
<param name="export_style" value="matchms"/>
121-
<output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
122-
</test>
123-
<test>
124-
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
125-
<param name="harmonization_metadata" value="True"/>
126127
<param name="export_peak_comments" value="False"/>
128+
<param name="export_style" value="matchms"/>
129+
</conditional>
130+
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
131+
<param name="harmonization_metadata" value="False"/>
132+
<output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
133+
</test>
134+
135+
<!-- Test 4: Convert to MSP with harmonization -->
136+
<test>
137+
<conditional name="output_file">
127138
<param name="output_format" value="msp"/>
139+
<param name="export_peak_comments" value="False"/>
128140
<param name="export_style" value="matchms"/>
129-
<output name="converted_library" file="convert/harmonized_msp_out.msp" ftype="msp"/>
130-
</test>
131-
<test>
132-
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
133-
<param name="harmonization_metadata" value="True"/>
134-
<param name="export_peak_comments" value="True"/>
141+
</conditional>
142+
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
143+
<param name="harmonization_metadata" value="True"/>
144+
<output name="converted_library" file="convert/harmonized_msp_out.msp" ftype="msp"/>
145+
</test>
146+
147+
<!-- Test 5: Convert to MSP with peak comments -->
148+
<test>
149+
<conditional name="output_file">
135150
<param name="output_format" value="msp"/>
151+
<param name="export_peak_comments" value="True"/>
136152
<param name="export_style" value="matchms"/>
137-
<output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
138-
</test>
139-
<test>
140-
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
141-
<param name="harmonization_metadata" value="True"/>
142-
<param name="export_peak_comments" value="False"/>
153+
</conditional>
154+
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
155+
<param name="harmonization_metadata" value="True"/>
156+
<output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
157+
</test>
158+
159+
<!-- Test 6: Convert to MSP with ms-lima style -->
160+
<test>
161+
<conditional name="output_file">
143162
<param name="output_format" value="msp"/>
163+
<param name="export_peak_comments" value="False"/>
144164
<param name="export_style" value="ms_lima"/>
145-
<output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
146-
</test>
147-
</tests>
165+
</conditional>
166+
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
167+
<param name="harmonization_metadata" value="True"/>
168+
<output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
169+
</test>
170+
</tests>
148171

149172

150173
<help><![CDATA[

‎tools/matchms/matchms_fingerprint_similarity.xml‎

Lines changed: 15 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_fingerprint_similarity" name="matchms fingerprint similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_fingerprint_similarity" name="matchms fingerprint similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors</description>
33

44
<macros>
@@ -60,20 +60,28 @@ scores.to_json("$scores_out")
6060

6161
<tests>
6262
<test>
63-
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
64-
<param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/>
63+
<conditional name="scores">
64+
<param name="use_scores" value="False"/>
65+
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
66+
<param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/>
67+
</conditional>
6568
<param name="fingerprint_similarity" value="dice" />
6669
<output name="scores_out" value="fingerprints/dice.json" ftype="json" />
6770
</test>
6871
<test>
69-
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
70-
<param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/>
72+
<conditional name="scores">
73+
<param name="use_scores" value="False"/>
74+
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
75+
<param name="references" value="similarity/rcx_exposome_pesticides_subset.msp" ftype="msp"/>
76+
</conditional>
7177
<param name="fingerprint_similarity" value="cosine" />
7278
<output name="scores_out" value="fingerprints/cosine.json" ftype="json" />
7379
</test>
7480
<test>
75-
<param name="use_scores" value="True"/>
76-
<param name="scores_in" value="metadata_match/inner_join_ri_20.json" ftype="json"/>
81+
<conditional name="scores">
82+
<param name="use_scores" value="True"/>
83+
<param name="scores_in" value="metadata_match/inner_join_ri_20.json" ftype="json"/>
84+
</conditional>
7785
<param name="fingerprint_similarity" value="jaccard" />
7886
<output name="scores_out" value="fingerprints/jaccard_scores.json" ftype="json" />
7987
</test>

‎tools/matchms/matchms_formatter.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>reformat scores object of matchms to long format table</description>
33

44
<macros>
@@ -50,20 +50,20 @@ result.to_csv('$output', sep="\t", index=False)
5050
<param label="Key" name="key" type="text" value="compound_name" help="Name of the key to use. Default is 'compound_name'." />
5151
</inputs>
5252
<outputs>
53-
<data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
53+
<data label="${tool.name} on ${on_string}" name="output" format="tabular"/>
5454
</outputs>
5555

5656
<tests>
5757
<test>
5858
<param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
5959
<param name="key" value="compound_name"/>
60-
<output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
60+
<output name="output" value="formatter/fill2_formatted.tsv" ftype="tabular"
6161
checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
6262
</test>
6363
<test>
6464
<param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
6565
<param name="key" value="compound_name"/>
66-
<output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
66+
<output name="output" file="formatter/test4_formatted.tsv" ftype="tabular"/>
6767
</test>
6868
</tests>
6969

‎tools/matchms/matchms_metadata_export.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>extract all metadata from mass spectra file to tabular format</description>
33
<macros>
44
<import>macros.xml</import>
@@ -43,19 +43,19 @@ data.to_csv("${output_file}", sep='\t', index=False)
4343
</inputs>
4444

4545
<outputs>
46-
<data label="matchms extract metadata on ${on_string}" name="output_file" format="tsv"/>
46+
<data label="matchms extract metadata on ${on_string}" name="output_file" format="tabular"/>
4747
</outputs>
4848

4949
<tests>
5050
<test>
5151
<param name="input_file" value="convert/mgf_out.mgf" ftype="mgf"/>
5252
<param name="harmonize_metadata" value="True"/>
53-
<output name="output_file" file="convert/metadata.tsv" ftype="tsv" compare="sim_size" delta="0"/>
53+
<output name="output_file" file="convert/metadata.tsv" ftype="tabular" compare="sim_size" delta="0"/>
5454
</test>
5555
<test>
5656
<param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
5757
<param name="harmonize_metadata" value="True"/>
58-
<output name="output_file" file="convert/metadata.tsv" ftype="tsv" compare="sim_size" delta="0"/>
58+
<output name="output_file" file="convert/metadata.tsv" ftype="tabular" compare="sim_size" delta="0"/>
5959
</test>
6060
</tests>
6161

‎tools/matchms/matchms_metadata_match.xml‎

Lines changed: 55 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>matchms metadata match calculation for numeric fields based on tolerance</description>
33

44
<macros>
@@ -85,45 +85,75 @@ scores.to_json("$scores_out")
8585

8686
<tests>
8787
<test>
88-
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
89-
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
90-
<param name="tolerance" value="60.0" />
88+
<conditional name="scores">
89+
<param name="use_scores" value="False"/>
90+
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
91+
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
92+
</conditional>
93+
<conditional name="matching">
94+
<param name="matching_type" value="difference" />
95+
<param name="tolerance" value="60.0" />
96+
</conditional>
9197
<output name="scores_out" value="metadata_match/ri_match_60.json" ftype="json" />
9298
</test>
9399
<test>
94-
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
95-
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
96-
<param name="matching_type" value="equal_match" />
97-
<param name="metadata_match_field" value="smiles" />
100+
<conditional name="scores">
101+
<param name="use_scores" value="False"/>
102+
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
103+
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
104+
</conditional>
105+
<conditional name="matching">
106+
<param name="matching_type" value="equal_match" />
107+
<param name="metadata_match_field" value="smiles" />
108+
</conditional>
98109
<output name="scores_out" value="metadata_match/smiles.json" ftype="json" />
99110
</test>
100111
<test>
101-
<param name="use_scores" value="True"/>
102-
<param name="scores_in" value="metadata_match/smiles.json" ftype="json"/>
103-
<param name="matching_type" value="equal_match" />
104-
<param name="metadata_match_field" value="inchikey" />
105-
<param name="join_type" value="inner" />
112+
<conditional name="scores">
113+
<param name="use_scores" value="True"/>
114+
<param name="scores_in" value="metadata_match/smiles.json" ftype="json"/>
115+
<param name="join_type" value="inner" />
116+
</conditional>
117+
<conditional name="matching">
118+
<param name="matching_type" value="equal_match" />
119+
<param name="metadata_match_field" value="inchikey" />
120+
</conditional>
106121
<output name="scores_out" value="metadata_match/inchi_key_inner.json" ftype="json" />
107122
</test>
108123
<test>
109-
<param name="use_scores" value="True"/>
110-
<param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
111-
<param name="tolerance" value="20.0" />
112-
<param name="join_type" value="inner" />
124+
<conditional name="scores">
125+
<param name="use_scores" value="True"/>
126+
<param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
127+
<param name="join_type" value="inner" />
128+
</conditional>
129+
<conditional name="matching">
130+
<param name="matching_type" value="difference" />
131+
<param name="tolerance" value="20.0" />
132+
</conditional>
113133
<output name="scores_out" value="metadata_match/inner_join_ri_20.json" ftype="json" />
114134
</test>
115135
<test>
116-
<param name="use_scores" value="True"/>
117-
<param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
118-
<param name="tolerance" value="20.0" />
119-
<param name="join_type" value="left" />
136+
<conditional name="scores">
137+
<param name="use_scores" value="True"/>
138+
<param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
139+
<param name="join_type" value="left" />
140+
</conditional>
141+
<conditional name="matching">
142+
<param name="matching_type" value="difference" />
143+
<param name="tolerance" value="20.0" />
144+
</conditional>
120145
<output name="scores_out" value="metadata_match/left_join_ri_20.json" ftype="json" />
121146
</test>
122147
<test>
123-
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
124-
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
125-
<param name="matching_type" value="equal_match" />
126-
<param name="metadata_match_field" value="formula" />
148+
<conditional name="scores">
149+
<param name="use_scores" value="False"/>
150+
<param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
151+
<param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
152+
</conditional>
153+
<conditional name="matching">
154+
<param name="matching_type" value="equal_match" />
155+
<param name="metadata_match_field" value="formula" />
156+
</conditional>
127157
<output name="scores_out" value="metadata_match/formula.json" ftype="json" />
128158
</test>
129159
</tests>

‎tools/matchms/matchms_remove_key.xml‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
1+
<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
22
<description>Remove metadata entry for all spectra in a library</description>
33

44
<macros>
@@ -60,7 +60,9 @@ matchms.exporting.save_as_msp(new_spectra, "${output}")
6060
<tests>
6161
<test>
6262
<param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
63-
<param name="key" value="ionmode"/>
63+
<repeat name="attribute_repeat">
64+
<param name="key" value="ionmode"/>
65+
</repeat>
6466
<output name="output" file="remove_key/out_matchms_remove_key.msp" ftype="msp"/>
6567
</test>
6668
<test>

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