Mercurial > repos > recetox > mfassignr_mfassign
comparison mfassignr_mfassign.xml @ 5:0492fff60960 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 1e98df2131b9b5384ca2e4310f93270eae6f517c
| author | recetox |
|---|---|
| date | Tue, 22 Oct 2024 07:25:13 +0000 |
| parents | 5aa9380f397b |
| children |
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| 4:4422c60a4b71 | 5:0492fff60960 |
|---|---|
| 1 <tool id="mfassignr_mfassign" name="MFAssignR MFAssign" version="@TOOL_VERSION@+galaxy0" profile="23.0"> | 1 <tool id="mfassignr_mfassign" name="MFAssignR MFAssign" version="@TOOL_VERSION@+galaxy1" profile="23.0"> |
| 2 <description>Molecular formula assignment.</description> | 2 <description>Molecular formula assignment.</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <import>help.xml</import> | 5 <import>help.xml</import> |
| 6 </macros> | 6 </macros> |
| 17 mono <- read.delim("$input_mono", sep="\t") | 17 mono <- read.delim("$input_mono", sep="\t") |
| 18 #if $input_iso | 18 #if $input_iso |
| 19 iso <- read.delim("$input_iso", sep="\t") | 19 iso <- read.delim("$input_iso", sep="\t") |
| 20 #end if | 20 #end if |
| 21 SN = $sn_ratio * $kmdn | 21 SN = $sn_ratio * $kmdn |
| 22 POEx = 0 | |
| 23 NOEx = 0 | |
| 24 | |
| 25 #if "$assign_typeof_ions"=="yes" | |
| 26 #if $ionMode=="pos" | |
| 27 POEx = 1 | |
| 28 NOEx = 0 | |
| 29 #else | |
| 30 POEx = 0 | |
| 31 NOEx = 1 | |
| 32 #end if | |
| 33 #end if | |
| 22 | 34 |
| 23 MF_assign <- MFAssignR::MFAssign( | 35 MF_assign <- MFAssignR::MFAssign( |
| 24 peaks = mono, | 36 peaks = mono, |
| 25 #if $input_iso | 37 #if $input_iso |
| 26 isopeaks = iso, | 38 isopeaks = iso, |
| 27 #end if | 39 #end if |
| 28 ionMode = "$ionmode", | 40 ionMode = "$ionmode", |
| 29 lowMW = $lowMW, | 41 lowMW = $lowMW, |
| 30 highMW = $highMW, | 42 highMW = $highMW, |
| 31 ppm_err = $ppm_err, | 43 ppm_err = $ppm_err, |
| 32 SN = SN | 44 SN = SN, |
| 45 POEx = POEx, | |
| 46 NOEx = NOEx, | |
| 47 Nx = $Nx, | |
| 48 Sx = $Sx, | |
| 49 Px = $Px, | |
| 50 S34x = $S34x, | |
| 51 N15x = $N15x, | |
| 52 Dx = $Dx, | |
| 53 Clx = $Clx, | |
| 54 Fx = $Fx, | |
| 55 Cl37x = $Cl37x, | |
| 56 Br81x = $Br81x, | |
| 57 Ix = $Ix, | |
| 58 Ex = $Ex, | |
| 59 Mx = $Mx, | |
| 60 NH4x = $NH4x, | |
| 61 Zx = $Zx, | |
| 62 Ox = $Ox, | |
| 63 O_Cmin = $O_Cmin, | |
| 64 O_Cmax = $O_Cmax, | |
| 65 H_Cmin = $H_Cmin, | |
| 66 H_Cmax = $H_Cmax, | |
| 67 DBEOmin = $DBEOmin, | |
| 68 DBEOmax = $DBEOmax, | |
| 69 Omin = $Omin, | |
| 70 max_def = $max_def, | |
| 71 min_def = $min_def, | |
| 72 HetCut = "$HetCut", | |
| 73 NMScut = "$NMScut", | |
| 74 DeNovo = $DeNovo, | |
| 75 nLoop = $nLoop, | |
| 76 Ambig = "$ambig_bool", | |
| 77 MSMS = "$MSMS", | |
| 78 Sval = $Sval, | |
| 79 Nval = $Nval, | |
| 80 S34val = $S34val, | |
| 81 N15val = $N15val, | |
| 82 Pval = $Pval, | |
| 83 iso_err = $iso_err, | |
| 84 SulfCheck = "$SulfCheck", | |
| 85 S34_abund = $S34_abund, | |
| 86 C13_abund = $C13_abund, | |
| 87 N3corr = "$N3corr" | |
| 33 ) | 88 ) |
| 34 | 89 |
| 35 write.table(MF_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t") | 90 write.table(MF_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t") |
| 36 write.table(MF_assign[['Ambig']], file = '$Ambig', row.names= FALSE, sep = "\t") | 91 write.table(MF_assign[['Ambig']], file = '$Ambig', row.names= FALSE, sep = "\t") |
| 37 write.table(MF_assign[['None']], file = '$None', row.names= FALSE, sep = "\t") | 92 write.table(MF_assign[['None']], file = '$None', row.names= FALSE, sep = "\t") |