Mercurial > repos > recetox > qcxms_getres

annotate msp_out.sh @ 0:ef51824f6d04 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
author recetox
date Fri, 08 Mar 2024 10:55:44 +0000
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ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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1 #!/bin/sh
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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2
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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3 molname=`sed -n '1{p;q}' molname.txt`
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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4 kword=$(grep 'NPOINTS' result.jdx)
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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5 num_peaks=$(echo "$kword" | sed 's/^[^=]*=//')
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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6 echo `pwd`
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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7 sed -n '/PEAK/,/END/{/PEAK/!{/END/!p}}' result.jdx > temp.dat
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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8 awk '{print $1, $2}' temp.dat > tempa.dat
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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9 sed "1s/^/NAME: $molname\nNum Peaks: $num_peaks\n/" tempa.dat >> simulated_spectra.msp
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
10 sed -i '$a\ ' simulated_spectra.msp
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
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11 rm temp.dat tempa.dat