diff mfassignr_mfassignCHO.xml @ 5:59326d3b9c52 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 1e98df2131b9b5384ca2e4310f93270eae6f517c

--- a/mfassignr_mfassignCHO.xml	Mon Oct 21 09:06:25 2024 +0000
+++ b/mfassignr_mfassignCHO.xml	Tue Oct 22 07:24:55 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="mfassignr_mfassignCHO" name="MFAssignR MFAssignCHO" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+<tool id="mfassignr_mfassignCHO" name="MFAssignR MFAssignCHO" version="@TOOL_VERSION@+galaxy1" profile="23.0">
     <description>Molecular formula assignment (only with CHO).</description>
     <macros>
         <import>macros.xml</import>
@@ -22,6 +22,18 @@
         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_CHO_assign <- MFAssignR::MFAssignCHO(
             peaks = mono,
@@ -32,7 +44,29 @@
             lowMW = $lowMW,
             highMW = $highMW,
             ppm_err = $ppm_err,
-            SN = SN
+            SN = SN,
+            POEx = POEx, 
+            NOEx = NOEx,
+            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"
         )
 
         write.table(MF_CHO_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t")
@@ -52,7 +86,7 @@
                help= "Data frame containing monoisotopic masses, output from the IsoFiltR function"/>
         <param name="input_iso" optional="true" type="data" format="tabular" label="Data frame of isotopic masses"
                help= "Data frame containing isotopic masses, output from the IsoFiltR function"/>
-        <expand macro="mfassign_param"/>
+        <expand macro="mfassigncho_param"/>
     </inputs>
     <outputs>
         <data name="Unambig" format="tabular" label="Unambiguous assignments by ${tool.name} on ${on_string}"/>