# HG changeset patch # User iuc # Date 1697884171 0 # Node ID 02e802817d48834bb62daa84561414974e59da84 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd diff -r 000000000000 -r 02e802817d48 mzmine_batch.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzmine_batch.xml Sat Oct 21 10:29:31 2023 +0000 @@ -0,0 +1,129 @@ + + + 3.6.0 + 0 + + + mzmine + + + mzmine + + > input.txt && + #end for + + #if $libraries + mkdir -p libraries && + #for $l in $libraries + #set escaped_l = re.sub('[^\s\w\-\.]', '_', str($l.element_identifier)) + ln -s '$l' 'libraries/$escaped_l'.$l.ext && + echo 'libraries/$escaped_l'.$l.ext >> libraries.txt && + #end for + #end if + ## modify output paths in batch XML to relative path + ## - any output will be redirected to ./output/BASENAME + mkdir -p output/ && + + sed -e 's@.*[\\\/]$[^\\\/]\+$@./output/\1@' '$batch' > batch.xml && + + mzmine + --batch 'batch.xml' + --input 'input.txt' + #if $libraries + --libraries 'libraries.txt' + #end if + --memory "\${MZMINE_MEMORY:-none}" + --temp "\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}" + --threads \${GALAXY_SLOTS:-1} +## ignored parameters +## -p,--pref preferences file +## -r,--running keep MZmine running in headless mode +## -tdfpseudoprofile Loads pseudo-profile frame spectra for tdf files +## instead of centroided spectra. +## -tsfprofile Loads profile spectra from .tsf data instead of +## centroid spectra. + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1038/s41587-023-01690-2 + + \ No newline at end of file diff -r 000000000000 -r 02e802817d48 test-data/test_small.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_small.xml Sat Oct 21 10:29:31 2023 +0000 @@ -0,0 +1,637 @@ + + + + /tmp/mzminetest/DOM_a.mzML + /tmp/mzminetest/DOM_b.mzXML + + + + + + + + 1 + + Any + ANY + + + + + 3.0 + + + 3000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + + + + + + + + + + + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + + + 3.0 + + + 3000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + + + + + + + + + + + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + false + + + /tmp/mzminetest/GNPS-FAULKNERLEGACY.json + + + + + + + + + + + 1 + + Any + ANY + + All scan types + + + 3.0 + + + 3000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + + + + + + + + + + + + + + 30000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + false + + + + + + + + + + 3 + + Any + ANY + + All scan types + + + 3.0 + + + 3000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + 1000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + + + + + + + + + + + + + + 3000.0 + + H,C,N,O,S + + 0.0015 + 3.0 + + 2 + + + + false + + + + + + + + + 0.5 + 10.0 + + + 1 + + Any + ANY + + 5 + 300000.0 + 500000.0 + + 0.002 + 10.0 + + eics + + + + + r + KEEP + + + 0.01 + 10.0 + + 0.05 + 0.25 + 1 + true + false + 6000.0 + 0.01 + + Retention time + 0.8420000000000001 + 0.05 + 0.0 + 500000.0 + 2.0 + + 0.0 + 1.501 + + 5 + + + + Aligned feature list + + 0.0015 + 5.0 + + 3.0 + 0.1 + 1.0 + 1.0 + 0.0 + false + false + + + 0.001 + 5.0 + + 0.0 + 0.0 + + + + 0.001 + 10.0 + + 2 + + + MassBank (mz^2 * I^0.5) + 0.65 + KEEP ALL AND MATCH TO ZERO + + + MassBank (mz^2 * I^0.5) + 0.7 + KEEP ALL AND MATCH TO ZERO + + + + KEEP + + + + 0.055000003 + 0.0 + 30000.0 + + + 2 + 0.0 + + + 0 + 0.0 + + 0.6 + true + + + 5 + 2 + PEARSON + 0.85 + 0.5 + + + 2 + PEARSON + 0.7 + + + + + + + 0.0015 + 3.0 + + ALL FEATURES + 0.0 + + POSITIVE + 2 + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3 + true + 4 + true + false + + + + + + MS level ≥ 2 (merged) + + 0.01 + 20.0 + + + 0.01 + 20.0 + + true + 4 + + + SQRT (mz^0 * I^0.5) + 0.1 + KEEP ALL AND MATCH TO ZERO + + + MassBank (mz^2 * I^0.5) + 0.7 + KEEP ALL AND MATCH TO ZERO + + + + + 0.05 + + + 0.001 + 5.0 + + false + 1 + + 3 + false + + + + + + /tmp/mzminetest/test2_iimn_gnps + + + across samples + weighted average (remove outliers) + sum intensities + + 0.001 + 5.0 + + 0.7 + 0.2 + 0.0 + 3.0 + + MS2 OR ION IDENTITY + Area + SIMPLE + + + true + HIGHRES + + + + + true + + false + + + + + D:\tmp\export_mzmine3\test2_sirius.MGF + D:\tmp\new_sirius\merged_new_sirius.mgf + D:\tmp\test\merged_new_sirius.mgf + + + across samples + weighted average (remove outliers) + sum intensities + + 0.001 + 5.0 + + 0.7 + 0.2 + 0.0 + 3.0 + + + 0.002 + 5.0 + + false + false + false + +