Mercurial > repos > recetox > qcxms_getres

annotate msp_out.sh @ 2:53dce0e49af7 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 68505a19637f8374cc5bde7e6b9370647a064ca9
author recetox
date Thu, 25 Jul 2024 14:27:08 +0000
parents ef51824f6d04
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
1 #!/bin/sh
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
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2
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
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
parents:
diff changeset
4 kword=$(grep 'NPOINTS' result.jdx)
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
5 num_peaks=$(echo "$kword" | sed 's/^[^=]*=//')
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
6 echo `pwd`
ef51824f6d04 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
recetox
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
11 rm temp.dat tempa.dat