Mercurial > repos > recetox > mfassignr_mfassign
changeset 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 | 4422c60a4b71 |
| children | 22c80f584bb1 |
| files | macros.xml mfassignr_mfassign.xml |
| diffstat | 2 files changed, 171 insertions(+), 3 deletions(-) [+] |
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--- a/macros.xml Mon Oct 21 09:06:40 2024 +0000 +++ b/macros.xml Tue Oct 22 07:25:13 2024 +0000 @@ -84,7 +84,7 @@ </param> </xml> - <xml name="mfassign_param"> + <xml name="mfassign_required_shared"> <param name="ppm_err" type="integer" label="ppm_err" help= "Error tolerance (ppm) for formula assignment" value="3"/> <expand macro="ionmode_param" /> @@ -95,6 +95,119 @@ help= "Upper limit of molecular mass to be assigned."/> </xml> + <xml name="mfassign_elements_shared"> + <param name="Mx" type="integer" label="Amount of Sodium adduct" value="0" help= "Sets the amount of Sodium adduct to be used in assignment."/> + <param name="NH4x" type="integer" label="Amount of Ammonium adduct" value="0" help= "Sets the amount of Ammonium adduct to be used in assignment."/> + <param name="Ox" type="integer" label="Maximum number of oxygen looked for in the CHOFIT core" value="30" help= "Sets the maximum number of oxygen looked for in the CHOFIT core, it limits the number of loops performed."/> + </xml> + + <xml name="mfassign_ratios_shared"> + <param name="O_Cmin" type="float" label="Minimum allowed O/C ratio" value="0" help= "Sets the minimum allowed oxygen to carbon ratio."/> + <param name="O_Cmax" type="float" label="Upper limit for O/C ratio" value="2.5" help= "Sets the upper limit for oxygen to carbon ratio."/> + <param name="H_Cmin" type="float" label="Lower limit for H/C ratio" value="0.1" help= "Sets the lower limit for hydrogen to carbon ratio."/> + <param name="H_Cmax" type="float" label="Upper limit for H/C ratio" value="3" help= "Sets the upper limit for hydrogen to carbon ratio for assigned formulas."/> + </xml> + + <xml name="mfassign_advanced_shared"> + <param name="Zx" type="integer" label="Amount of charge" min="1" max="5" value="1" help= "Sets the amount of charge to be used in assignment."/> + <param name="assign_typeof_ions" type="select" display="radio" label="Assign odd electron ions based on the ionization mode?" help="This parameter determines whether to assign either positive mode odd electron ions (if ionMode is positive) or negative mode odd electron ions (if ionMode is negative)."> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <param name="DBEOmin" type="float" label="Lower limit for DBE minus oxygen QA parameter" value="-13" help= "Sets the lower limit for double bond equivalent (DBE) minus oxygen QA parameter."/> + <param name="DBEOmax" type="float" label="Upper limit for DBE minus oxygen QA parameter" value="13" help= "Sets the upper limit for double bond equivalent (DBE) minus oxygen QA parameter."/> + <param name="Omin" type="integer" min="0" label="Lower limit for number of O in assigned formula" value="0" help= "Sets the lower limit for oxygen number in assigned formula."/> + <param name="max_def" type="float" min="0" max="1" label="Upper limit for KMD" value="0.9" help= "Sets the upper limit of mass defect for using floor() instead of round() for KMD."/> + <param name="min_def" type="float" min="0" max="1" label="Lower limit for KMD" value="0.5" help= "Sets the lower limit of mass defect for using floor() instead of round() for KMD."/> + <param name = "HetCut" type="select" display="radio" label="Turn on the high heteroatom QA parameter?" help= "HetCut turns on or off the high heteroatom QA parameter."> + <option value="on">yes</option> + <option value="off" selected="true">no</option> + </param> + <param name = "NMScut" type="select" display="radio" label="NMScut" help= "Turn on the nominal mass series QA parameter?"> + <option value="on" selected="true">yes</option> + <option value="off">no</option> + </param> + <param name="nLoop" type="integer" min="1" label="Number of times the KMD and z* series assignment loops" value="5" help= "Sets the number of times the KMD and z* series assignment loops."/> + <param name="ambig_bool" type="select" display="radio" label="Turn on the increased ambiguity for assignment?" help= "Turns on or off increased ambiguity for assignment."> + <option value="on">yes</option> + <option value="off" selected="true">no</option> + </param> + <param name = "MSMS" type="select" display="radio" label="Turn on the CH2 KMD prescreening before initial assignment?" help= "Turns on or off CH2 KMD prescreening before initial assignment."> + <option value="on" >yes</option> + <option value="off" selected="true">no</option> + </param> + </xml> + + <xml name="mfassign_valence_param"> + <param name="Sval" type="integer" label="Valence of Sulphur" value="2" help= "Sets the valence of Sulfur."/> + <param name="Nval" type="integer" label="Valence of Nitrogen" value="3" help= "Sets the valence of Nitrogen."/> + <param name="S34val" type="integer" label="Valence of Sulphur 34" value="2" help= "Sets the valence of Sulfur 34."/> + <param name="N15val" type="integer" label="Valence of Nitrogen 15" value="3" help= "Sets the valence of Nitrogen 15."/> + <param name="Pval" type="integer" label="Valence of Phosphorus" value="5" help= "Sets the valence of Phosphorus."/> + </xml> + + <xml name="mfassigncho_param"> + <expand macro="mfassign_required_shared" /> + <section name="advanced" title="Advanced" expanded="false"> + <section name="elements_amount" title="Set amount of elements" expanded="false"> + <param name="Ex" type="integer" label="Amount of Chlorine 37" value="0" help= "Sets the amount of Chlorine 37 to be used in assignment."/> + <expand macro="mfassign_elements_shared" /> + </section> + <section name="set_ratios" title="Set the ratios" expanded="false"> + <expand macro="mfassign_ratios_shared" /> + </section> + <section name="other_params" title="Other" expanded="false"> + <expand macro="mfassign_advanced_shared" /> + <param name="DeNovo" type="float" label="De novo cut point for the data" value="1000" help= "Sets the de novo cut point for the data."/> + </section> + </section> + </xml> + + <xml name="mfassign_param"> + <expand macro="mfassign_required_shared" /> + <section name="advanced" title="Advanced" expanded="false"> + <section name="elements_amount" title="Set amount of elements" expanded="false"> + <param name="Nx" type="integer" label="Amount of Nitrogen 14" value="0" help= "Sets the maximum allowable number of Nitrogen 14 to be used in assign"/> + <param name="Sx" type="integer" label="Amount of Sulphur 32" value="0" help= "Sets the maximum allowable number of Sulfur 32 to be used in assign"/> + <param name="Px" type="integer" label="Amount of Phosphorus 31" value="0" help= "Sets the maximum allowable number of Phosphorus 31 to be used in assign"/> + <param name="Ex" type="integer" label="Amount of Carbon 13" value="0" help= "Sets the amount of Carbon 13 to be used in assignment."/> + <param name="S34x" type="integer" label="Amount of Sulfur 34" value="0" help= "Sets the amount of Sulfur 34 to be used in assignment."/> + <param name="N15x" type="integer" label="Amount of Nitrogen 15" value="0" help= "Sets the amount of Nitrogen 15 to be used in assignment."/> + <param name="Dx" type="integer" label="Amount of Deuterium" value="0" help= "Sets the amount of Deuterium to be used in assignment."/> + <param name="Clx" type="integer" label="Amount of Chlorine" value="0" help= "Sets the amount of Chlorine to be used in assignment."/> + <param name="Fx" type="integer" label="Amount of Fluorine" value="0" help= "Sets the amount of Fluorine to be used in assignment."/> + <param name="Cl37x" type="integer" label="Amount of Chlorine 37" value="0" help= "Sets the amount of Chlorine 37 to be used in assignment."/> + <param name="Br81x" type="integer" label="Amount of Bromine 81" value="0" help= "Sets the amount of Bromine 81 to be used in assignment."/> + <param name="Ix" type="integer" label="Amount of Iodine 127" value="0" help= "Sets the amount of Iodine 127 to be used in assignment."/> + <expand macro="mfassign_elements_shared" /> + </section> + + <section name="set_valence" title="Set the valence" expanded="false"> + <expand macro="mfassign_valence_param"/> + </section> + + <section name="set_ratios" title="Set the ratios" expanded="false"> + <expand macro="mfassign_ratios_shared" /> + <param name="S34_abund" type="integer" min="0" max="100" label="Maximum 34S/32S isotope ratio" value="30" help= "Sets the maximum 34S/32S isotope ratio (in percent) for isotope matching."/> + <param name="C13_abund" type="integer" min="0" max="100" label="Maximum 13C/12C isotope ratio" value="60" help= "Sets the maximum 13C/12C isotope ratio (in percent) for isotope matching."/> + </section> + + <section name="other_params" title="Other" expanded="false"> + <param name="iso_err" type="integer" min="0" max="20" label="Error tolerance (ppm) for polyisotope matching" value="3" help= "Sets the the error tolerance (ppm) for polyisotope matching."/> + <expand macro="mfassign_advanced_shared" /> + <param name = "SulfCheck" type="select" display="radio" label="Turn on the sulfur isotope check?" help= "Turns on or off the sulfur isotope check QA parameter.c"> + <option value="on" selected="true">yes</option> + <option value="off">no</option> + </param> + <param name = "N3corr" type="select" display="radio" label="Turn on the correction of N3OS monoisotopic assignments to 13C assignment?" help= "Turns on or off correction of N3OS monoisotopic assignments to 13C assignment."> + <option value="on" selected="true">yes</option> + <option value="off">no</option> + </param> + <param name="DeNovo" type="float" label="De novo cut point for the data" value="300" help= "Sets the de novo cut point for the data."/> + </section> + </section> + </xml> + <xml name="findrecalseries_param"> <param name="input_file" type="data" format="tabular" label="Input data" help= "Recalibration series, output from RecalList"/>
--- a/mfassignr_mfassign.xml Mon Oct 21 09:06:40 2024 +0000 +++ b/mfassignr_mfassign.xml Tue Oct 22 07:25:13 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="mfassignr_mfassign" name="MFAssignR MFAssign" version="@TOOL_VERSION@+galaxy0" profile="23.0"> +<tool id="mfassignr_mfassign" name="MFAssignR MFAssign" version="@TOOL_VERSION@+galaxy1" profile="23.0"> <description>Molecular formula assignment.</description> <macros> <import>macros.xml</import> @@ -19,6 +19,18 @@ iso <- read.delim("$input_iso", sep="\t") #end if SN = $sn_ratio * $kmdn + POEx = 0 + NOEx = 0 + + #if "$assign_typeof_ions"=="yes" + #if $ionMode=="pos" + POEx = 1 + NOEx = 0 + #else + POEx = 0 + NOEx = 1 + #end if + #end if MF_assign <- MFAssignR::MFAssign( peaks = mono, @@ -29,7 +41,50 @@ lowMW = $lowMW, highMW = $highMW, ppm_err = $ppm_err, - SN = SN + SN = SN, + POEx = POEx, + NOEx = NOEx, + Nx = $Nx, + Sx = $Sx, + Px = $Px, + S34x = $S34x, + N15x = $N15x, + Dx = $Dx, + Clx = $Clx, + Fx = $Fx, + Cl37x = $Cl37x, + Br81x = $Br81x, + Ix = $Ix, + Ex = $Ex, + Mx = $Mx, + NH4x = $NH4x, + Zx = $Zx, + Ox = $Ox, + O_Cmin = $O_Cmin, + O_Cmax = $O_Cmax, + H_Cmin = $H_Cmin, + H_Cmax = $H_Cmax, + DBEOmin = $DBEOmin, + DBEOmax = $DBEOmax, + Omin = $Omin, + max_def = $max_def, + min_def = $min_def, + HetCut = "$HetCut", + NMScut = "$NMScut", + DeNovo = $DeNovo, + nLoop = $nLoop, + Ambig = "$ambig_bool", + MSMS = "$MSMS", + Sval = $Sval, + Nval = $Nval, + S34val = $S34val, + N15val = $N15val, + Pval = $Pval, + iso_err = $iso_err, + SulfCheck = "$SulfCheck", + S34_abund = $S34_abund, + C13_abund = $C13_abund, + N3corr = "$N3corr" ) write.table(MF_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t")