changeset 14:018f73a9e98e draft

planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219

--- a/CAMERA.r	Thu Mar 30 09:02:43 2017 -0400
+++ b/CAMERA.r	Fri Mar 31 11:20:26 2017 -0400
@@ -144,7 +144,7 @@
         listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,
         diffrepP=diffrepP,diffrepN=diffrepN,
         pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],
-        intval=listArguments[["intval"]], convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]],
+        convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]],
         variableMetadataOutput=variableMetadataOutput
     )
 }

--- a/abims_CAMERA_combinexsAnnos.xml	Thu Mar 30 09:02:43 2017 -0400
+++ b/abims_CAMERA_combinexsAnnos.xml	Fri Mar 31 11:20:26 2017 -0400
@@ -19,7 +19,9 @@
 
         pos $pos tol $tol ruleset $ruleset keep_meta $keep_meta
 
-        @COMMAND_PEAKLIST@
+        convertRTMinute $export.convertRTMinute
+        numDigitsMZ $export.numDigitsMZ
+        numDigitsRT $export.numDigitsRT
 
     ]]></command>
 
@@ -36,7 +38,11 @@
         <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
         <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
 
-        <expand macro="input_peaklist"/>
+        <section name="export" title="Export options">
+            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+        </section>
     </inputs>
 
     <outputs>
@@ -54,7 +60,11 @@
             <param name="pos" value="TRUE"/>
             <param name="tol" value="2"/>
             <param name="ruleset" value="1,1"/>
-            <expand macro="test_peaklist"/>
+            <section name="export">
+                <param name="convertRTMinute" value="True"/>
+                <param name="numDigitsMZ" value="4" />
+                <param name="numDigitsRT" value="1" />
+            </section>
             <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
         </test>
     </tests>

--- a/lib.r	Thu Mar 30 09:02:43 2017 -0400
+++ b/lib.r	Fri Mar 31 11:20:26 2017 -0400
@@ -157,7 +157,7 @@
 }
 
 
-combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, intval="into", convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
+combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
 
     #Load the two Rdata to extract the xset objects from positive and negative mode
     cat("\tObject xset from positive mode\n")
@@ -192,7 +192,7 @@
         mode="pos. Mode"
     }
 
-    peakList=getPeaklist(xa,intval=intval)
+    peakList=getPeaklist(xa)
     peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
     variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
     variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]

--- a/macros.xml	Thu Mar 30 09:02:43 2017 -0400
+++ b/macros.xml	Fri Mar 31 11:20:26 2017 -0400
@@ -107,7 +107,7 @@
             <param name="maxiso" value="4"/>
             <param name="minfrac" value="0.5"/>
         </section>
-        <section name="general">
+        <section name="findgeneral">
             <param name="ppm" value="5"/>
             <param name="mzabs" value="0.015"/>
             <param name="max_peaks" value="100"/>
@@ -127,7 +127,7 @@
         <expand macro="test_peaklist"/>
     </xml>
 
-    <xml name="test_annotate_diffreport_quick">
+    <xml name="test_annotate_quick_false">
         <param name="quick" value="FALSE"/>
         <section name="groupcorr">
             <param name="cor_eic_th" value="0.75"/>
@@ -139,6 +139,12 @@
         </section>
     </xml>
 
+    <xml name="test_annotate_quick_true">
+        <conditional name="quick_block">
+            <param name="quick" value="TRUE"/>
+        </conditional>
+    </xml>
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark