# HG changeset patch
# User recetox
# Date 1770198200 0
# Node ID 0f01dc62c4f3422c7bd215c0567e7339ec35fad4
planemo upload for repository https://github.com/rdurnik/aoptk commit df42dbae2ad18cec86a3b927123fdc3f1c82287c
diff -r 000000000000 -r 0f01dc62c4f3 aoptk_publication_tracker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/aoptk_publication_tracker.xml Wed Feb 04 09:43:20 2026 +0000
@@ -0,0 +1,112 @@
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+ Tool to track publications.
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+ macros.xml
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+ ^\d+(\.\d+)*\.?$
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+ 10.1093/bioinformatics/btp163
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\ No newline at end of file
diff -r 000000000000 -r 0f01dc62c4f3 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Feb 04 09:43:20 2026 +0000
@@ -0,0 +1,108 @@
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+ 0.1.6
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+ aoptk
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+ [0-9a-zA-Z_ ()*'"[\]\[\]\-:.\[\]α-ωΑ-Ω]+
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+from matchms.importing import load_from_msp, scores_from_json
+from matchms import Scores
+#if $scores.use_scores == "True"
+scores = scores_from_json("$scores_in")
+join_type = "$scores.join_type"
+#else
+scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
+join_type = "left"
+#end if
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+from matchms import set_matchms_logger_level
+set_matchms_logger_level("WARNING")
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/chemicals_per_publication_test.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/master_test.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/publications_per_chemical.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/read1.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/read2.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/read3.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/read_test.xlsx
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diff -r 000000000000 -r 0f01dc62c4f3 test-data/updated_master_table.xlsx
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