Mercurial > repos > mmonsoor > camera_combinexsannos
changeset 14:018f73a9e98e draft
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
author | lecorguille |
---|---|
date | Fri, 31 Mar 2017 11:20:26 -0400 |
parents | 97e2c754e81f |
children | ab50b1130b61 |
files | CAMERA.r abims_CAMERA_combinexsAnnos.xml lib.r macros.xml |
diffstat | 4 files changed, 24 insertions(+), 8 deletions(-) [+] |
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--- 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