maldi_quant_preprocessing: maldi_quant_preprocessing.xml annotate

annotate maldi_quant_preprocessing.xml @ 4:60ee8c592b13 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc

author	galaxyp
date	Sat, 04 Mar 2023 19:14:31 +0000
parents	71411ac28268
children

rev	line source
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.0">
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	2 <description>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	3 Preprocessing of mass-spectrometry imaging data
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	4 </description>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	5 <macros>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	6 <import>maldi_macros.xml</import>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	7 </macros>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	8 <expand macro="requirements"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	9 <command detect_errors="exit_code">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	10 <![CDATA[
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	11 cat '${maldi_quant_preprocessing}' &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	12 #if $infile.ext == 'imzml'
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	13 cp '${infile.extra_files_path}/imzml' infile.imzML &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	14 cp '${infile.extra_files_path}/ibd' infile.ibd &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	15 #elif $infile.ext == 'analyze75'
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	16 cp '${infile.extra_files_path}/hdr' infile.hdr &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	17 cp '${infile.extra_files_path}/img' infile.img &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	19 du infile.hdr &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	20 du infile.img &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	21 du -s -B1 infile.hdr &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	22 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	23 Rscript "${maldi_quant_preprocessing}" &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	24
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	25 mkdir $outfile_imzml.files_path &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	26 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" \| true &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	27 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" \| true &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	28 echo "imzML file:" > $outfile_imzml &&
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	29 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	30 ]]>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	31 </command>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	32 <configfiles>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	33 <configfile name="maldi_quant_preprocessing"><![CDATA[
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	34
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	35 @R_IMPORTS@
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	36
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	37 #if $restriction_conditional.restriction == 'restrict':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	38
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	39 print('Reading mask region')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	40 ## Import imzML file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	41
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	42 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	43 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	44
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	45 maldi_data = importImzMl('infile.imzML',
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	46 coordinates = coordinate_matrix)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	47 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	48
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	49 #else:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	50
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	51 print('Reading entire file')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	52 #if $infile.ext == 'imzml'
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	53 ## Import imzML file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	54 maldi_data = import( 'infile.imzML', type="imzML" )
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	55 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	56 #elif $infile.ext == 'analyze75'
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	57 ## Import analyze7.5 file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	58 maldi_data = importAnalyze( 'infile.hdr' )
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	59 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	60 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	61
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	62 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	63
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	64 ## Quality control plots during preprocessing
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	65
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	66 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	67 plot(0,type='n',axes=FALSE,ann=FALSE)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	68
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	69 ## if no filename is given, name of file in Galaxy history is used
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	70 #set $filename = $infile.display_name
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	71 title(main=paste("$filename"))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	72
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	73
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	74 #################### Preprocessing methods #####################################
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	75
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	76 ## QC plot on input file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	77 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	78 plot(avgSpectra, main="Average spectrum for input file")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	79
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	80 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	81 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	82 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	83 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	84 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	85 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	86 inputdata = c(minmz, maxmz,number_features,mean_features,medint, pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	87 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, pixel_number))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	88 vectorofactions = "inputdata"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	89
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	90
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	91 #for $method in $methods:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	92
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	93 #if str( $method.methods_conditional.method ) == 'Transformation':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	94
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	95 print('transforming')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	96 ##transformation
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	97 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	98 ## QC plot and numbers
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	99 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	100 plot(avgSpectra, main="Average spectrum after transformation")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	101 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	102 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	103 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	104 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	105 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	106 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	107 transformed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	108 QC_numbers= cbind(QC_numbers, transformed)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	109 vectorofactions = append(vectorofactions, "transformed")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	110
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	111
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	112 #elif str( $method.methods_conditional.method ) == 'Smoothing':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	113
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	114 print('smoothing')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	115 ##smoothing
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	116
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	117 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	118 print('SavitzkyGolay')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	119
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	120 maldi_data = smoothIntensity(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	121 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	122 halfWindowSize=$method.methods_conditional.halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	123
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	124 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	125 print('MovingAverage')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	126
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	127 maldi_data = smoothIntensity(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	128 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	129 halfWindowSize=$method.methods_conditional.halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	130
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	131 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	132
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	133 ## QC plot and numbers
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	134 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	135 plot(avgSpectra, main="Average spectrum after smoothing", sub="")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	136 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	137 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	138 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	139 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	140 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	141 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	142 smoothed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	143 QC_numbers= cbind(QC_numbers, smoothed)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	144 vectorofactions = append(vectorofactions, "smoothed")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	145
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	146
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	147 #elif str( $method.methods_conditional.method ) == 'Baseline':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	148
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	149 print('baseline removing')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	150 ## Remove baseline
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	151
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	152 ## Choose random spectra for QC plots
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	153 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	154
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	155 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	156 print('SNIP')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	157
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	158 par(mfrow = c(2,2))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	159 for (random_sample in random_spectra){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	160 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	161 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	162 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	163 lines(maldi_data_baseline, col="blue", lwd=2)}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	164
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	165 maldi_data = removeBaseline(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	166 method="SNIP",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	167 iterations=$method.methods_conditional.methods_for_baseline.iterations)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	168
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	169
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	170 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	171 print('TopHat')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	172
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	173 par(mfrow = c(2,2))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	174 for (random_sample in random_spectra){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	175 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	176 method="TopHat", halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	177 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	178 lines(maldi_data_baseline, col="blue", lwd=2)}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	179
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	180 maldi_data = removeBaseline(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	181 method="TopHat",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	182 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	183
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	184
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	185 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	186 print('ConvexHull')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	187
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	188 par(mfrow = c(2,2))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	189 for (random_sample in random_spectra){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	190 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	191 method="ConvexHull")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	192 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	193 lines(maldi_data_baseline, col="blue", lwd=2)}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	194
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	195 maldi_data = removeBaseline(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	196 method="ConvexHull")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	197
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	198
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	199 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	200 print('median')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	201
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	202 par(mfrow = c(2,2))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	203 for (random_sample in random_spectra){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	204 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	205 method="median", halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	206 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	207 lines(maldi_data_baseline, col="blue", lwd=2)}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	208
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	209 maldi_data = removeBaseline(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	210 method="median",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	211 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	212
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	213 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	214
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	215 ## QC plot and numbers
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	216 par(mfrow = c(1,1))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	217 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	218 plot(avgSpectra, main="Average spectrum after baseline removal")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	219 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	220 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	221 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	222 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	223 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	224 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	225 baseline_removed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	226 QC_numbers= cbind(QC_numbers, baseline_removed)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	227 vectorofactions = append(vectorofactions, "bl_removed")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	228
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	229
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	230 #elif str( $method.methods_conditional.method ) == 'Calibrate':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	231
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	232 print('calibrate')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	233 ##calibrate
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	234
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	235 #if str($method.methods_conditional.cond_calibration_range) == "yes":
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	236 ## calibrate only given m/z range
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	237 maldi_data = calibrateIntensity(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	238 method="$method.methods_conditional.calibrate_method",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	239 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	240 #else:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	241 maldi_data = calibrateIntensity(maldi_data,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	242 method="$method.methods_conditional.calibrate_method")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	243 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	244 ## QC plot and numbers
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	245 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	246 plot(avgSpectra, main="Average spectrum after normalization")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	247 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	248 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	249 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	250 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	251 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	252 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	253 intensity_calibrated = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	254 QC_numbers= cbind(QC_numbers, intensity_calibrated)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	255 vectorofactions = append(vectorofactions, "calibrated")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	256
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	257
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	258 #elif str( $method.methods_conditional.method ) == 'Align':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	259
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	260 print('align')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	261 ##align spectra with 3 separate functions
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	262
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	263 ## create reference if needed
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	264
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	265 ## 1) detect peaks:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	266 peaks <- detectPeaks(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	267 method="$method.methods_conditional.peak_method", SNR=$method.methods_conditional.snr)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	268
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	269
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	270 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	271
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	272 ## 2) calculate warping:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	273 warping_function <- determineWarpingFunctions(peaks,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	274 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	275 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	276
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	277 ## 3) warp spectra:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	278 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	279
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	280
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	281 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	282
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	283 ## create reference mass_vector from tabular file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	284 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,$method.methods_conditional.reference_for_alignment.mz_column]
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	285 int_vector = rep(1,length(mass_vector))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	286 mass_list = createMassPeaks(mass_vector, int_vector)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	287
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	288 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	289 print('default alignment')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	290
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	291 ## 2) calculate warping:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	292 warping_function <- determineWarpingFunctions(peaks,
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	293 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	294 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	295
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	296 ## 3) warp spectra:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	297 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	298
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	299 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	300 print('spectra wise alignment')
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	301
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	302 maldi_data_new_list =list()
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	303
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	304 for (pixelnb in 1:length(peaks))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	305 {
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	306 ## 2) calculate warping:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	307 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	308 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	309 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	310
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	311 ## 3) warp spectra:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	312 maldi_data_new = warpMassSpectra(list(maldi_data[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	313 maldi_data_new_list = c(maldi_data_new_list, maldi_data_new)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	314
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	315 }
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	316 maldi_data = maldi_data_new_list
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	317 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	318 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	319
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	320
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	321 #if $method.methods_conditional.remove_empty:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	322 print(paste(length(findEmptyMassObjects(maldi_data)), " empty spectra were removed", sep=" "))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	323
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	324 ## only if there are empty spectra to remove
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	325
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	326 if (length(findEmptyMassObjects(maldi_data))>0)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	327
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	328 {
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	329 maldi_data = removeEmptyMassObjects(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	330 }
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	331 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	332
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	333 ## QC plot
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	334
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	335 if (length(maldi_data)>0){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	336 avgSpectra = averageMassSpectra(maldi_data,method="mean")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	337 plot(avgSpectra, main="Average spectrum after alignment")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	338 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	339 }else{print("All spectra are empty")}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	340
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	341 pixel_number = length(maldi_data)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	342 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	343 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	344 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	345
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	346 number_features = length(unique(unlist(lapply(maldi_data,mass))))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	347 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint,pixel_number)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	348 QC_numbers= cbind(QC_numbers, spectra_aligned)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	349 vectorofactions = append(vectorofactions, "aligned")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	350
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	351 #elif str( $method.methods_conditional.method ) == 'skip_preprocessing':
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	352 ##for now as option to filter large files
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	353
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	354 #end if
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	355
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	356 #end for
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	357
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	358 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity", "pixel\nnumber")
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	359 colnames(QC_numbers) = vectorofactions
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	360 plot(0,type='n',axes=FALSE,ann=FALSE)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	361 grid.table(t(QC_numbers))
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	362
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	363 dev.off()
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	364
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	365 ## export imzML file
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	366 if (length(maldi_data)>0){
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	367 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	368
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	369 }else{"All spectra are empty, outputfiles will be empty,too."}
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	370
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	371 ]]>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	372 </configfile>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	373 </configfiles>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	374 <inputs>
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	375 <param name="infile" type="data" format="imzml,analyze75" label="MSI data" help="Input file as imzML (composite upload). The file must be in profile mode, not centroided."/>
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	376 <conditional name="restriction_conditional">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	377 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	378 <option value="no_restriction" selected="True">No, calculate on entire file</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	379 <option value="restrict">Yes, restrict to spectra of interest</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	380 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	381 <when value="restrict">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	382 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	383 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	384 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	385 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	386 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	387 <when value="no_restriction"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	388 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	389 <repeat name="methods" title="Method" min="1">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	390 <conditional name="methods_conditional">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	391 <param name="method" type="select" label="Select a method">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	392 <option value="Transformation" selected="True">Transformation</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	393 <option value="Smoothing">Smoothing</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	394 <option value="Baseline">Baseline removal</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	395 <option value="Calibrate">Intensity calibration (normalization)</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	396 <option value="Align">Align spectra (warping/phase correction)</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	397 <option value="skip_preprocessing">Skip preprocessing</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	398 <validator type="empty_field" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	399 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	400 <when value="Transformation">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	401 <param name="transform_method" type="select" label="Transformation method">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	402 <option value="sqrt" selected="True">sqrt</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	403 <option value="log">log</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	404 <option value="log2">log2</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	405 <option value="log10">log10</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	406 <validator type="empty_field" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	407 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	408 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	409 <when value="Smoothing">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	410 <conditional name="methods_for_smoothing">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	411 <param name="smooth_method" type="select" label="Smoothing method" help="This method smoothes the intensity values of a MassSpectrum object.">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	412 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	413 <option value="MovingAverage">MovingAverage</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	414 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	415 <when value="SavitzkyGolay">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	416 <param name="polynomial" value="3" type="text" label="Polynomial order"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	417 help="Controls the order of the filter, should be smaller than the resulting window."/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	418 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	419 <when value="MovingAverage">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	420 <param name="weighted" type="boolean" label="Weighted average" help = "Indicates if the average should be equal weight or if it should have weights depending on the distance from the center as calculated as 1/2^abs(-halfWindowSize:halfWindowSize) with the sum of all weigths normalized to 1" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	421 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	422 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	423 <param name="halfWindowSize" type="integer" value="10"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	424 label="Half window size"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	425 help="Number of data points, the resulting window reaches from
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	426 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	427 (window size is 2*halfWindowSize+1)."/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	428 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	429 <when value="Baseline">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	430 <conditional name="methods_for_baseline">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	431 <param name="baseline_method" type="select" label="Baseline removal method">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	432 <option value="SNIP" selected="True">SNIP</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	433 <option value="TopHat">TopHat</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	434 <option value="ConvexHull">ConvexHull</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	435 <option value="median">median</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	436 <validator type="empty_field" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	437 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	438 <when value="SNIP">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	439 <param name="iterations" type="integer" value="100"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	440 label="Number of iterations" help="Corresponds to half window size: The resulting window reaches from mass[cur_index-iterations] to mass[cur_index+iterations]"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	441 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	442 <when value="TopHat">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	443 <param name="tophat_halfWindowSize" type="integer" value="10"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	444 label="Half window size"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	445 help="Number of data points, the resulting window reaches from
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	446 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	447 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	448 <when value="ConvexHull"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	449 <when value="median">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	450 <param name="median_halfWindowSize" type="integer" value="10"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	451 label="Half window size"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	452 help="Number of data points, the resulting window reaches from
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	453 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	454 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	455 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	456 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	457 <when value="Calibrate">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	458 <param name="calibrate_method" type="select" label="Intensity calibration method" help="Intensity normalization">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	459 <option value="TIC" selected="True">TIC</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	460 <option value="PQN">PQN</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	461 <option value="median">median</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	462 <validator type="empty_field" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	463 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	464 <conditional name="cond_calibration_range">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	465 <param name="calibration_range" type="select" label="m/z range" help="Instead of the whole m/z range, a specified m/z range can be used to calculate the scaling factor.">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	466 <option value="no" selected="True">complete m/z range</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	467 <option value="yes">specify a m/z range</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	468 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	469 <when value="no"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	470 <when value="yes">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	471 <param name="mass_start" type="integer" value="800"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	472 label="Start of m/z range, has to be inside m/z range"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	473 help="Scaling factor is calculated on the mass range and applied to the whole spectrum."/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	474 <param name="mass_end" type="integer" value="3000"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	475 label="End of m/z range, has to be inside m/z range"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	476 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	477 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	478 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	479 <when value="Align">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	480 <param name="warping_method" type="select" label="Alignment method">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	481 <option value="lowess" selected="True">Lowess</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	482 <option value="linear">Linear</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	483 <option value="quadratic">Quadratic</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	484 <option value="cubic">Cubic</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	485 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	486
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	487 <param name="tolerance" type="float" value="0.00005"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	488 label="Tolerance"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	489 help="abs(mz1 - mz2)/mz2, maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	490
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	491 <param name="halfWindowSize" type="integer" value="20"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	492 label="Half window size"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	493 help="Number of data points, the resulting window reaches from
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	494 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	495 (window size is 2*halfWindowSize+1).
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	496 The best size differs depending on the selected smoothing method."/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	497
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	498 <param name="peak_method" type="select" label="Noise estimation function">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	499 <option value="MAD" selected="True">MAD</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	500 <option value="SuperSmoother">SuperSmoother</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	501 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	502
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	503 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	504 <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	505 <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	506 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE"/>
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	507
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	508 <conditional name="reference_for_alignment">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	509 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	510 <option value="no_reference" selected="True">no reference</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	511 <option value="yes_reference">reference from tabular file</option>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	512 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	513 <when value="no_reference">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	514 <param name="min_frequency" type="float" value="0.9" label = "minFrequency" help="Removal of all peaks which occur in less than minFrequency spectra to generate the reference m/z"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	515 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	516 <when value="yes_reference">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	517 <param name="reference_file" type="data" format="tabular"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	518 label="Reference m/z values"
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	519 help="Tabular file"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	520 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	521 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	522 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	523 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	524 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	525 </when>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	526 <when value="skip_preprocessing"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	527 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	528 </repeat>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	529 <param name="export_processed" type="boolean" label="Export processed imzML" help="otherwise continuous imzML will be exported" truevalue="TRUE" falsevalue="FALSE"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	530 </inputs>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	531 <outputs>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	532 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" />
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	533 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${tool.name} on ${on_string}: QC"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	534 </outputs>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	535 <tests>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	536 <test>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	537 <param name="infile" value="" ftype="imzml">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	538 <composite_data value="Example_Continuous.imzML"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	539 <composite_data value="Example_Continuous.ibd"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	540 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	541 <conditional name="restriction_conditional">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	542 <param name="restriction" value="restrict"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	543 <param name="coordinates_file" value="restricted_pixels.tabular"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	544 <param name="column_x" value="1"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	545 <param name="column_y" value="2"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	546 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	547 <conditional name="methods_conditional">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	548 <param name="method" value="Transformation"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	549 <param name="transform_method" value="log2"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	550 <param name="method" value="Smoothing"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	551 <param name="smooth_method" value="SavitzkyGolay"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	552 <param name="method" value="Basline"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	553 <param name="baseline_method" value ="TopHat"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	554 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	555 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4">
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	556 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="8"/>
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	557 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	558 </output>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	559 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	560 </test>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	561 <test>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	562 <param name="infile" value="" ftype="imzml">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	563 <composite_data value="Example_Continuous.imzML"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	564 <composite_data value="Example_Continuous.ibd"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	565 </param>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	566 <conditional name="methods_conditional">
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	567 <param name="method" value="Calibrate"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	568 <param name="calibrate_method" value="median"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	569 </conditional>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	570 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4">
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	571 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="8"/>
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	572 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	573 </output>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	574 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	575 </test>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	576 </tests>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	577 <help><![CDATA[
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	578
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	579 @MADLI_QUANT_DESCRIPTION@
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	580
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	581 -----
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	582
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	583 Input data
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	584
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	585 - MSI data: 2 types of input data can be used:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	586
4 60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc galaxyp parents: 3 diff changeset	587 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
3 71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	588
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	589 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	590
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	591 ::
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	592
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	593 x_coord y_coord
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	594 1 1
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	595 2 1
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	596 3 1
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	597 ...
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	598 ...
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	599
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	600 - Optional: Tabular file with reference m/z for the spectra align function. At least 2 m/z values of the input list must be present in every spectrum to peform the alignment. First column must contain m/z values, without empty fields or letters. Tabular files with any header name or no header at all are supported.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	601
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	602 ::
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	603
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	604
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	605 m/z
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	606 100.0
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	607 100.01
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	608 100.02
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	609 ...
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	610 ...
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	611
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	612
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	613
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	614 Options
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	615
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	616 - Transformation: Variance stabilization through intensity transformation:'log', 'log2', 'log10' and 'squareroot' (sqrt) are available
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	617 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are 'SavitzkyGolay' and 'Moving Average'
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	618
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	619 - For all smoothing methods: The larger the 'Half window size', the stronger the smoothing. The resulting window should be smaller than the FWHM (full width at half maximum) of the typical peaks. Moving average needs smaller window size than SavitzkyGolay.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	620 - Moving average: Recommended for broader peaks/high m/z range spectra. Weighted moving average: Points in the center get larger weight factors than points away from the center.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	621 - SavitzkyGolay: Recommended for sharp peaks/low m/z range, preserves the shape of the local maxima. The PolynomialOrder should be smaller than the resulting window. Negative values will be replaced with 0.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	622
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	623 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets).
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	624
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	625 - Available methods are SNIP, TopHat,ConvexHull and median:
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	626 - SNIP is the default baseline reduction method in MALDIquant.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	627 - ConvexHull is not appropriate for MALDI-TOF baseline removal.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	628 - The moving median may generate negative intensities.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	629 - Except for the ConvexHull all methods have a parameter for the 'Half window size' (in SNIP it is called 'iterations'). The smaller the window the more baseline will be removed but also parts of the peaks. Wider windows preserve the peak height better and produce a smoother baseline, but some local background variation will remain.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	630
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	631 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	632
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	633 - TIC and median are local calibration methods: each spectrum is normalized on its own (each peak is divided by the TIC or median of the spectrum)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	634 - PQN is a global calibration method: In PQN all spectra are calibrated using the TIC calibration first. Subsequently, a median reference spectrum is created and the intensities in all spectra are standardized using the reference spectrum and a spectrum-specific median is calculated for each spectrum. Finally, each spectrum is rescaled by the median of the ratios of its intensity values and that of the reference spectrum
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	635
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	636 - Spectra alignment (warping): alignment for (re)calibration of m/z values.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	637
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	638 - peak detection is performed, the reference peaks will be matched to those detected peaks
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	639 - without external reference m/z: internal reference is obtained by filtering and binning the picked peaks to find landmark peaks and their average m/z
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	640 - with external reference m/z: the given m/z are used as a reference, at least 10 reference values are recommended
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	641 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the present (picked) peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. To prevent an error when this criterium is not fullfilled, "Don't throw an error when less than 2 reference m/z were found in a spectrum" should be set to yes. If the not aligned spectra should be set to zero select yes in "If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes.
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	642
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	643
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	644 Output
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	645
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	646 - imzML file (imzML format can be continuous or processed)
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	647 - PDF with average mass spectra after each preprocessing step
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	648
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	649 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	650
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	651 ]]>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	652 </help>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	653 <expand macro="citation"/>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	654 </tool>
71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	655

Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate maldi_quant_preprocessing.xml @ 4:60ee8c592b13 draft default tip