diff XSeekerPreparator.xml @ 19:2937e72e5891 draft

" master branch Updating"

--- a/XSeekerPreparator.xml	Tue Feb 01 18:09:11 2022 +0000
+++ b/XSeekerPreparator.xml	Tue Oct 18 12:57:28 2022 +0000
@@ -1,14 +1,9 @@
-<tool id="xseeker_preparator"
-      name="XSeeker Preparator"
-      version="1.2.4"
->
-    <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
-    
+<tool id="xseeker_preparator" name="XSeeker Preparator" version="1.3.0">
+    <description>prepares RData file from XCMS+CAMERA for XSeeker</description>
     <edam_operations>
         <edam_operation>operation_1812</edam_operation>
         <edam_operation>operation_0335</edam_operation>
     </edam_operations>
-    
     <requirements>
         <requirement type="package" >bioconductor-xcms</requirement>
         <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
@@ -36,58 +31,47 @@
          -->
     </requirements>
     <stdio>
-
         <exit_code 
             range="1"
             level="warning"
             description="Selected samples have no data associated to them."
         />
-
         <exit_code 
             range="2"
             level="warning"
             description="Some samples have no data associated to them."
         />
-
     </stdio>
-
     <version_command>
         Rscript '$__tool_directory__/XSeekerPreparator.R' -v
     </version_command>
-
     <command>
         <![CDATA[
             Rscript '$__tool_directory__/XSeekerPreparator.R'
-
                 -P
-
                 --input '$input'
                 --output '$output'
-
                 #if $samples.selected
                     --samples '${",".join($samples.selected)}'
                 #end if
-
                 #if $database.archetypes
                     --archetype '${",".join($database.archetypes)}'
                 #end if
-
                 #if $database.base.kind == "tabular"
                     --compounds-csv '${database.base.tabular}'
                 #else if $database.base.kind == "sql"
                     --database '${database.base.sql}'
                 #end if
-
                 #if $database.models.kind == "default"
                     --models '${base_config}'
                 #else
                     --models '${database.models.url}'
                 #end if
-
+                #if $class_column
+                    --class '${class_column}'
+                #end if
         ]]>
-
     </command>
-
     <inputs>
         <param 
             name="input"
@@ -98,6 +82,18 @@
             format="rdata"
         >
         </param>
+        <param
+            name="class_column"
+            type="text"
+            value=""
+            label="Column class name"
+            help="
+                The name of the column containing the classes - 
+                leave empty to let xsprep guess
+            "
+            optional="true"
+        >
+        </param>
         <section name="samples" title="Samples Options" expanded="false">
             <param 
                 name="selected"
@@ -109,7 +105,6 @@
             >
             </param>
         </section>
-
         <section name="database" title="Database Options" expanded="false">
             <param
                 name="archetypes"
@@ -120,7 +115,6 @@
                 <option value="G" selected="true">General</option>
                 <option value="H">Halogenates</option>
             </param>
-
             <conditional name="base">
                 <param name="kind" type="select" label="File containing compound's type">
                     <option value="none" selected="true">None (deafult)</option>
@@ -150,7 +144,6 @@
                     </param>
                 </when>
             </conditional>
-
             <conditional name="models">
                 <param name="kind" type="select" label="How is the database's model defined">
                     <option value="default" selected="true">Default (regular XSeeker Database)</option>
@@ -166,13 +159,10 @@
             </conditional>
         </section>
     </inputs>
-
-
     <outputs>
         <data format="sqlite" name="output" />
         <!-- <data format="xseeker.sqlite" name="output" /> -->
     </outputs>
-
     <configfiles>
         <configfile name="base_config">
 tryCatch({
@@ -180,111 +170,113 @@
 }, error=function(e) {
     stop("Please, install DBModelR before you source this file.")
 })
-
 list(
-    adduct=DBModelR::ModelDefinition(
-        table="adduct",
-        fields=list(
-            name="TEXT",
-            mass="FLOAT",
-            charge="INTEGER",
-            multi="INTEGER",
-            formula_add="TEXT",
-            formula_ded="TEXT",
-            sign="TEXT",
-            oidscore="INTEGER",
-            quasi="INTEGER",
-            ips="FLOAT"
+    adduct = DBModelR::ModelDefinition(
+        table = "adduct",
+        fields = list(
+            name = "TEXT",
+            mass = "FLOAT",
+            charge = "INTEGER",
+            multi = "INTEGER",
+            formula_add = "TEXT",
+            formula_ded = "TEXT",
+            sign = "TEXT",
+            oidscore = "INTEGER",
+            quasi = "INTEGER",
+            ips = "FLOAT"
         )
     ),
-    cluster=DBModelR::ModelDefinition(
-        table="cluster",
-        fields=list(
-            clusterID="INTEGER",
-            formula="TEXT",
-            annotation="TEXT",
-            coeff="FLOAT",
-            r_squared="FLOAT",
-            charge="INTEGER",
-            mean_rt="FLOAT",
-            score="FLOAT",
-            deviation="FLOAT",
-            status="TEXT",
-            curent_group="INTEGER",
-            pc_group="INTEGER",
-            align_group="INTEGER",
-            xcms_group="INTEGER"
+    cluster = DBModelR::ModelDefinition(
+        table = "cluster",
+        fields = list(
+            clusterID = "INTEGER",
+            formula = "TEXT",
+            annotation = "TEXT",
+            coeff = "FLOAT",
+            r_squared = "FLOAT",
+            charge = "INTEGER",
+            mean_rt = "FLOAT",
+            score = "FLOAT",
+            deviation = "FLOAT",
+            status = "TEXT",
+            # adduct = "TEXT",
+            curent_group = "INTEGER",
+            pc_group = "INTEGER",
+            align_group = "INTEGER",
+            xcms_group = "INTEGER"
         ),
-        one=list("sample", "compound", "adduct")
+        one = list("compound", "adduct"),
+        many = list("sample")
     ),
-    compound=DBModelR::ModelDefinition(
-        table="compound",
-        fields=list(
-            name="TEXT",
-            common_name="TEXT",
-            formula="TEXT",
-            charge="INTEGER",
-            date="TEXT",
-            mz="FLOAT"
+    compound = DBModelR::ModelDefinition(
+        table = "compound",
+        fields = list(
+            name = "TEXT",
+            common_name = "TEXT",
+            formula = "TEXT",
+            charge = "INTEGER",
+            date = "TEXT",
+            mz = "FLOAT"
         )
     ),
-    feature=DBModelR::ModelDefinition(
-        table="feature",
-        fields=list(
-            featureID="INTEGER",
-            mz="FLOAT",
-            mz_min="FLOAT",
-            mz_max="FLOAT",
-            rt="FLOAT",
-            rt_min="FLOAT",
-            rt_max="FLOAT",
-            int_o="FLOAT",
-            int_b="FLOAT",
-            max_o="FLOAT",
-            iso="TEXT",
-            abundance="FLOAT"
+    feature = DBModelR::ModelDefinition(
+        table = "feature",
+        fields = list(
+            featureID = "INTEGER",
+            mz = "FLOAT",
+            mz_min = "FLOAT",
+            mz_max = "FLOAT",
+            rt = "FLOAT",
+            rt_min = "FLOAT",
+            rt_max = "FLOAT",
+            int_o = "FLOAT",
+            int_b = "FLOAT",
+            max_o = "FLOAT",
+            iso = "TEXT",
+            abundance = "FLOAT"
         ),
-        one=list("cluster")
+        one = list("cluster"),
+        many = list("sample")
     ),
-    instrument=DBModelR::ModelDefinition(
-        table="instrument",
-        fields=list(
-            model="TEXT",
-            manufacturer="TEXT",
-            analyzer="TEXT",
-            detector_type="TEXT",
-            ion_source="TEXT"
+    instrument = DBModelR::ModelDefinition(
+        table = "instrument",
+        fields = list(
+            model = "TEXT",
+            manufacturer = "TEXT",
+            analyzer = "TEXT",
+            detector_type = "TEXT",
+            ion_source = "TEXT"
         )
     ),
-    instrument_config=DBModelR::ModelDefinition(
-        table="instrument_config",
-        fields=list(
-            resolution="TEXT",
-            agc_target="TEXT",
-            maximum_IT="TEXT",
-            number_of_scan_range="TEXT",
-            scan_range="TEXT",
-            version="TEXT"
+    instrument_config = DBModelR::ModelDefinition(
+        table = "instrument_config",
+        fields = list(
+            resolution = "TEXT",
+            agc_target = "TEXT",
+            maximum_IT = "TEXT",
+            number_of_scan_range = "TEXT",
+            scan_range = "TEXT",
+            version = "TEXT"
         )
     ),
-    project=DBModelR::ModelDefinition(
-        table="project",
-        fields=list(
-            name="TEXT",
-            comment="TEXT"
+    project = DBModelR::ModelDefinition(
+        table = "project",
+        fields = list(
+            name = "TEXT",
+            comment = "TEXT"
         ),
-        one=list("sample")
+        one = list("sample")
     ),
-    sample=DBModelR::ModelDefinition(
-        table="sample",
-        fields=list(
-            name="TEXT",
-            path="TEXT",
-            polarity="TEXT",
-            kind="TEXT", ## rdata or mxml or enriched_rdata
-            raw="BLOB"
+    sample = DBModelR::ModelDefinition(
+        table = "sample",
+        fields = list(
+            name = "TEXT",
+            path = "TEXT",
+            polarity = "TEXT",
+            kind = "TEXT", ## rdata or mxml or enriched_rdata
+            raw = "BLOB"
         ),
-        one=list(
+        one = list(
             "peak_picking_parameters",
             "pairing_parameters",
             "alignmenmt_parameters",
@@ -295,56 +287,56 @@
             "smol_xcms_set"
         )
     ),
-    smol_xcms_set=DBModelR::ModelDefinition(
-        table="smol_xcms_set",
-        fields=list(
-            raw="BLOB"
+    smol_xcms_set = DBModelR::ModelDefinition(
+        table = "smol_xcms_set",
+        fields = list(
+            raw = "BLOB"
         )
     ),
-    software=DBModelR::ModelDefinition(
-        table="software",
-        fields=list(
-            name="TEXT",
-            version="TEXT"
+    software = DBModelR::ModelDefinition(
+        table = "software",
+        fields = list(
+            name = "TEXT",
+            version = "TEXT"
         )
     ),
-    peak_picking_parameters=DBModelR::ModelDefinition(
-        table="peak_picking_parameters",
-        fields=list(
-            ppm="FLOAT",
-            peakwidth="TEXT",
-            snthresh="TEXT",
-            prefilterStep="TEXT",
-            prefilterLevel="TEXT",
-            mzdiff="TEXT",
-            fitgauss="TEXT",
-            noise="TEXT",
-            mzCenterFun="TEXT",
-            integrate="INTEGER",
-            firstBaselineCheck="TEXT",
-            snthreshIsoROIs="TEXT",
-            maxCharge="INTEGER",
-            maxIso="INTEGER",
-            mzIntervalExtension="TEXT"
+    peak_picking_parameters = DBModelR::ModelDefinition(
+        table = "peak_picking_parameters",
+        fields = list(
+            ppm = "FLOAT",
+            peakwidth = "TEXT",
+            snthresh = "TEXT",
+            prefilterStep = "TEXT",
+            prefilterLevel = "TEXT",
+            mzdiff = "TEXT",
+            fitgauss = "TEXT",
+            noise = "TEXT",
+            mzCenterFun = "TEXT",
+            integrate = "INTEGER",
+            firstBaselineCheck = "TEXT",
+            snthreshIsoROIs = "TEXT",
+            maxCharge = "INTEGER",
+            maxIso = "INTEGER",
+            mzIntervalExtension = "TEXT"
         )
     ),
-    alignmenmt_parameters=DBModelR::ModelDefinition(
-        table="alignmenmt_parameters",
-        fields=list(
-            binSize="TEXT",
-            centerSample="TEXT",
-            response="TEXT",
-            distFun="TEXT",
-            gapInit="TEXT",
-            gapExtend="TEXT",
-            factorDiag="TEXT",
-            factorGap="TEXT",
-            localAlignment="INTEGER",
-            initPenalty="TEXT",
-            bw="TEXT",
-            minFraction="TEXT",
-            minSamples="TEXT",
-            maxFeatures="TEXT"
+    alignmenmt_parameters = DBModelR::ModelDefinition(
+        table = "alignmenmt_parameters",
+        fields = list(
+            binSize = "TEXT",
+            centerSample = "TEXT",
+            response = "TEXT",
+            distFun = "TEXT",
+            gapInit = "TEXT",
+            gapExtend = "TEXT",
+            factorDiag = "TEXT",
+            factorGap = "TEXT",
+            localAlignment = "INTEGER",
+            initPenalty = "TEXT",
+            bw = "TEXT",
+            minFraction = "TEXT",
+            minSamples = "TEXT",
+            maxFeatures = "TEXT"
         )
     )
 )