# HG changeset patch # User workflow4metabolomics # Date 1570528300 14400 # Node ID 963722c4e1dad3135aacb3dd4079411f4c988c3c "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" diff -r 000000000000 -r 963722c4e1da gen-test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gen-test.sh Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,3 @@ +genform ms=test-data/CreatineMs.txt out=test-data/CreatineMs.out exist out=test-data/CreatineMs.out acc=20 rej=30 + +genform ms=test-data/CreatineMs.txt msms=test-data/CreatineMsMs.txt exist oms=test-data/CreatineMsMs-oms.out omsms=test-data/CreatineMsMs-omsms.out oclean=test-data/CreatineMsMs-oclean.out out=test-data/CreatineMsMs.out acc=20 rej=30 analyze loss intens dbe cm pc sc diff -r 000000000000 -r 963722c4e1da genform.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genform.xml Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,496 @@ + + Generation of molecular formulas by high-resolution MS and MS/MS data + + 8 + + + genform + + '$out' + #else + && cp out '$out' + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + + + + + + + +

+ + + + +

+ + + + + addoutput['oms'] + + + addoutput['omsms'] + + + addoutput['oclean'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + +

+ + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_ for info. + + ]]> + + + 10.3390/metabo3020440 + @article{meringer2011ms, + title={MS/MS data improves automated determination of molecular formulas by mass spectrometry}, + author={Meringer, Markus and Reinker, Stefan and Zhang, Juan and Muller, Alban}, + journal={MATCH Commun. Math. Comput. Chem}, + volume={65}, + number={2}, + pages={259--290}, + year={2011} + } + + diff -r 000000000000 -r 963722c4e1da test-data/CreatineMs.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMs.out Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,1 @@ +C4H9N3O2 -0.8 0.96674 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMs.txt Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,2 @@ +132.07686 147049184 +133.08012 4004960.8 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMsMs-oclean.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMsMs-oclean.out Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,2 @@ + 111.02010 0.04273602 + 132.07730 1.00000000 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMsMs-oms.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMsMs-oms.out Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,2 @@ + 132.07686 0.97348659 + 133.08012 0.02651341 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMsMs-omsms.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMsMs-omsms.out Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,2 @@ + 111.02010 1.00000000 + 132.07730 1.00000000 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMsMs.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMsMs.out Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,3 @@ +C4H9N3O2 2 132.07675 -0.8 96.933 100.000 96.933 + 111.02010 0.04273602 -H7N 4.5 111.01890 -10.8 + 132.07730 1.00000000 no loss 1.5 132.07675 -4.1 diff -r 000000000000 -r 963722c4e1da test-data/CreatineMsMs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CreatineMsMs.txt Tue Oct 08 05:51:40 2019 -0400 @@ -0,0 +1,2 @@ +111.0201 71.07 +132.0773 1663