maldi_quant_peak_detection: maldi_quant_peakdetection.xml annotate

annotate maldi_quant_peakdetection.xml @ 5:af766257766e draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"

author	galaxyp
date	Thu, 19 Mar 2020 22:06:54 +0000
parents	c6b47c89a2f5
children	8431b33e6989

rev	line source
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.5">
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	2 <description>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	3 Peak detection, binning and filtering for mass-spectrometry imaging data
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	4 </description>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	5 <macros>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	6 <import>maldi_macros.xml</import>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	7 </macros>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	8 <expand macro="requirements"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	9 <command detect_errors="exit_code">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	10 <![CDATA[
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	11 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	14 #elif $infile.ext == 'analyze75'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	16 cp '${infile.extra_files_path}/img' infile.img &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	18 #else
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	19 ln -s '$infile' infile.RData &&
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	20 #end if
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	21 cat '${maldi_quant_peak_detection}' &&
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	22 Rscript '${maldi_quant_peak_detection}' &&
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	23 mkdir $outfile_imzml.files_path &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	24 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" \| true &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	25 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" \| true &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	26 echo "imzML file:" > $outfile_imzml &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	27 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	28 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	29 </command>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	30 <configfiles>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	31 <configfile name="maldi_quant_peak_detection"><![CDATA[
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	32
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	33 @R_IMPORTS@
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	34
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	35 #if $restriction_conditional.restriction == 'restrict':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	36
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	37 print('Reading mask region')
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	38
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	39 ## Import imzML file
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	40 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	41 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	42
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	43 maldi_data <- importImzMl('infile.imzML',
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	44 coordinates = coordinate_matrix, centroided = $centroids)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	45 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	46
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	47
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	48 #else:
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	49
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	50 print('Reading entire file')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	51 ## Import imzML file
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	52
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	53 #if $infile.ext == 'imzml'
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	54 print('imzML file')
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	55 #if str($centroids) == "TRUE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	56 peaks <- importImzMl('infile.imzML', centroided = $centroids)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	57 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	58 coordinates_info = cbind(coordinates(peaks)[,1:2], c(1:length(peaks)))
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	59 #else
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	60 maldi_data <- importImzMl('infile.imzML', centroided = $centroids)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	61 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	62 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	63 #end if
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	64
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	65
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	66 #elif $infile.ext == 'tabular'
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	67 print('tabular file')
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	68 #set $centroids = "TRUE" ## will be used in some if conditions
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	69 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	70 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	71 pixelnames = unique(peak_tabular\$spectrum)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	72
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	73 peaks = list()
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	74 for (spectra in 1:length(peak_list))
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	75 {
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	76 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	77 peaks[[spectra]] = single_peaks
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	78 }
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	79
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	80 #else
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	81 print('rdata file')
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	82 loadRData <- function(fileName){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	83 #loads an RData file, and returns it
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	84 load(fileName)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	85 get(ls()[ls() != "fileName"])
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	86 }
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	87 msidata = loadRData('infile.RData')
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	88 centroided(msidata) = $centroids
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	89 ## change to correct pixelnames
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	90
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	91 x_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 1))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	92 y_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 2))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	93 x_coordinates = gsub("x = ","",x_coords)
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	94 y_coordinates = gsub(" y = ","",y_coords)
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	95 pixelnames = paste0("xy_", x_coordinates, "_", y_coordinates)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	96
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	97 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	98
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	99 if (centroided(msidata) == FALSE){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	100 ## create mass spectrum object
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	101 cardinal_mzs = Cardinal::mz(msidata)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	102 maldi_data = list()
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	103 for(number_spectra in 1:ncol(msidata)){
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	104 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])}
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	105 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	106 }else{
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	107 peaks = list()
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	108 for (spectra in 1:ncol(msidata))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	109 {
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	110 single_peaks = createMassPeaks(Cardinal::mz(msidata), Cardinal::spectra(msidata)[,spectra], snr=as.numeric(rep("NA", nrow(msidata))))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	111 peaks[[spectra]] = single_peaks
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	112 }
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	113 coordinates_info = cbind(cardinal_coordinates, c(1:length(peaks)))}
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	114 #end if
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	115 #end if
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	116
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	117 ## default summarized = FALSE
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	118 summarized_spectra = FALSE
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	119
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	120 ## Quality control plots during peak detection
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	121 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	122 plot(0,type='n',axes=FALSE,ann=FALSE)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	123
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	124 ## if no filename is given, name of file in Galaxy history is used
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	125 #set $filename = $infile.display_name
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	126
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	127 title(main=paste("$filename"))
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	128
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	129 ## plot input file spectrum:
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	130 #if $centroids:
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	131 ## Choose random spectra for QC plots
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	132 print(length(peaks))
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	133 random_spectra = sample(1:length(peaks), 4, replace=FALSE)
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	134 random_spectra_name = pixelnames[random_spectra]
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	135 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	136 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	137 plot(peaks[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	138 title("Input spectra", outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	139
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	140 #else
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	141 ## Choose random spectra for QC plots
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	142 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	143 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	144 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	145 plot(maldi_data[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	146 }
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	147 title("Input spectra", outer=TRUE, line=0)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	148 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	149
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	150
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	151 ## QC numbers for input file
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	152 #if str($centroids) == "TRUE"
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	153 pixel_number = length(peaks)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	154 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	155 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	156 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	157 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	158 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	159 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	160 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	161 vectorofactions = "inputdata"
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	162 #else
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	163 pixel_number = length(maldi_data)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	164 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	165 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	166 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	167 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	168 number_features = length(unique(unlist(lapply(maldi_data,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	169 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	170 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	171 vectorofactions = "inputdata"
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	172 #end if
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	173
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	174 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	175
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	176 ## read and extract x,y,annotation information
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	177 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	178 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	179 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	180
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	181 ## merge provided annotation with coordinate information of MSI data
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	182 colnames(coordinates_info)[3] = "pixel_index"
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	183 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	184 merged_annotation[is.na(merged_annotation)] = "NA"
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	185 ## order coordinate information according to pixel index to make sure that the order stays the same
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	186 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	187 samples = as.factor(merged_annotation\$annotation)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	188
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	189 ## print annotation overview into PDF output
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	190
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	191 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	192 geom_tile() +
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	193 coord_fixed()+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	194 ggtitle("Spatial orientation of annotated data")+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	195 theme_bw()+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	196 theme(plot.title = element_text(hjust = 0.5))+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	197 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	198 theme(legend.position="bottom",legend.direction="vertical")+
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	199 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	200 theme(legend.position="bottom",legend.direction="vertical")+
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	201 guides(fill=guide_legend(ncol=4,byrow=TRUE))
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	202
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	203 print(combine_plot)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	204
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	205 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	206
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	207 #################### Preprocessing methods #####################################
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	208
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	209 #for $method in $methods:
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	210
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	211 #if str( $method.methods_conditional.method ) == 'Peak_detection':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	212 print('peak detection')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	213 ##peak detection
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	214
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	215 #if $method.methods_conditional.use_annotations:
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	216 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	217 pixelnames = levels(samples)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	218 summarized_spectra = TRUE
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	219 random_spectra = sample(1:length(maldi_data), 4, replace=TRUE)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	220 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	221
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	222 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	223 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	224
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	225 ## QC plot and numbers
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	226 ## plot old spectra with baseline in blue and picked peaks in green
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	227 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	228 for (random_sample in random_spectra){
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	229 noise = estimateNoise(maldi_data[[random_sample]], method= "$method.methods_conditional.peak_method")
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	230 plot(maldi_data[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	231 lines(noise[,1], noise[,2]*$method.methods_conditional.snr, col="blue")
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	232 points(peaks[[random_sample]], col="green", pch=20)}
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	233 title("S/N in blue and picked peaks in green", outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	234
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	235 ## plot new spectrum
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	236 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	237 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	238 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	239 title("Picked peaks", outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	240
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	241 pixel_number = length(peaks)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	242 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	243 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	244 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	245 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	246 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	247 peaks_picked = c(minmz, maxmz,number_features,mean_features, medint)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	248 QC_numbers= cbind(QC_numbers, peaks_picked)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	249 vectorofactions = append(vectorofactions, "peaks_picked")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	250
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	251 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	252 featureMatrix <- intensityMatrix(peaks)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	253 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	254 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	255 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	256 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	257 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	258 featureMatrix2 =cbind(pixelnames, featureMatrix)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	259 colnames(featureMatrix2)[1] = c("mz")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	260 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	261 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	262 }else{print("There are no spectra with peaks left")}
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	263
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	264
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	265 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	266
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	267 print('monoisotopic peaks')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	268 ##monoisotopic peaks
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	269
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	270 ## keep peaks to plot them with monoisotopic peaks
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	271 picked_peaks = peaks
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	272
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	273 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor,
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	274 tolerance=$method.methods_conditional.tolerance,
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	275 distance=c($method.methods_conditional.distance),
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	276 size=$method.methods_conditional.size)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	277
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	278 ## plot old spectrum with picked isotopes as green dots
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	279 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	280 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	281 plot(picked_peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	282 points(peaks[[random_sample]], col="green", pch=20)}
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	283 title(paste0("Monoisotopic peaks in green"), outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	284
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	285
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	286 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	287 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	288 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	289 title("Monoisotopic peaks", outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	290
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	291 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	292 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	293 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	294 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	295 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	296 monoisotopes = c(minmz, maxmz,number_features,mean_features, medint)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	297 QC_numbers= cbind(QC_numbers, monoisotopes)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	298 vectorofactions = append(vectorofactions, "monoisotopes")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	299
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	300 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	301 featureMatrix <- intensityMatrix(peaks)
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	302 ## only for profile imzML file: featurematrix is overwritten:
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	303 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	304 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	305 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	306 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	307 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	308 featureMatrix2 =cbind(pixelnames, featureMatrix)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	309 colnames(featureMatrix2)[1] = c("mz")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	310 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	311 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	312 }else{print("There are no spectra with peaks left")}
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	313
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	314
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	315
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	316 #elif str( $method.methods_conditional.method ) == 'Align':
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	317
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	318 print('align')
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	319 ##align spectra with 2 separate functions
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	320
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	321
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	322 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	323 ## 1) calculate warping:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	324 warping_function <- determineWarpingFunctions(peaks,
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	325 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	326 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	327 ## 2) warp spectra:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	328 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	329
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	330
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	331 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	332
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	333 ## create reference mass_vector from tabular file
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	334 mass_vector = read.delim("$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]
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	335 int_vector = rep(1,length(mass_vector))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	336 mass_list = createMassPeaks(mass_vector, int_vector)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	337
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	338 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	339 print('default alignment')
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	340
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	341 ## 1) calculate warping:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	342 warping_function <- determineWarpingFunctions(peaks,
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	343 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	344 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	345 ## 2) warp spectra:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	346 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	347
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	348 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	349 print('spectra wise alignment')
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	350
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	351 peaks_new_list =list()
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	352
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	353 for (pixelnb in 1:length(peaks))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	354 {
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	355
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	356 ## 1) calculate warping:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	357 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	358 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	359 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	360 ## 2) warp spectra:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	361 peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	362 }
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	363 peaks = peaks_new_list
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	364
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	365 #end if
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	366
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	367 #end if
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	368
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	369 #if $method.methods_conditional.remove_empty:
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	370 print(paste(length(findEmptyMassObjects(peaks)), " empty spectra were removed", sep=" "))
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	371
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	372 ## only if there are empty spectra to remove
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	373
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	374 if (length(findEmptyMassObjects(peaks))>0)
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	375
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	376 {
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	377 #if $infile.ext == 'rdata'
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	378 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(peaks),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	379 #end if
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	380
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	381 peaks = removeEmptyMassObjects(peaks)
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	382 }
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	383 #end if
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	384
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	385 ## QC plot and numbers
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	386 par(mfrow = c(2, 2), oma=c(0,0,2,0))
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	387
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	388 for (random_sample in random_spectra){
5 af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	389
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	390
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	391 tryCatch(
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	392 {
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	393 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))},
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	394 error=function(cond) {
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	395 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	396 }
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	397 )
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	398 }
af766257766e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e" galaxyp parents: 4 diff changeset	399
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	400 title("Aligned spectra", outer=TRUE, line=0)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	401 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	402 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	403 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	404 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	405 number_features = length(unique(unlist(lapply(peaks,mass))))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	406 aligned = c(minmz, maxmz,number_features,mean_features, medint)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	407 QC_numbers= cbind(QC_numbers, aligned)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	408 vectorofactions = append(vectorofactions, "aligned")
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	409
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	410 if (length(peaks[!sapply(peaks, isEmpty)])>0){
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	411 featureMatrix <- intensityMatrix(peaks)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	412 ## only for profile imzML file: featurematrix is overwritten:
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	413 #if $infile.ext == 'imzml'
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	414 #if str($centroids) == "FALSE"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	415 featureMatrix <- intensityMatrix(peaks, maldi_data)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	416 #end if
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	417 #end if
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	418 featureMatrix2 =cbind(pixelnames, featureMatrix)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	419 colnames(featureMatrix2)[1] = c("mz")
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	420 featureMatrix2 = t(featureMatrix2)
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	421 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	422 }else{print("There are no spectra with peaks left")}
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	423
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	424 #elif str( $method.methods_conditional.method ) == 'Binning':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	425
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	426 print('binning')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	427 ##m/z binning
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	428
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	429 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method")
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	430
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	431 ## QC plot and numbers
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	432 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	433 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	434 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	435 title("Binned spectra", outer=TRUE, line=0)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	436 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	437 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	438 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	439 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	440 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	441 binned = c(minmz, maxmz,number_features,mean_features, medint)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	442 QC_numbers= cbind(QC_numbers, binned)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	443 vectorofactions = append(vectorofactions, "binned")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	444
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	445 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	446 featureMatrix <- intensityMatrix(peaks)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	447 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	448 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	449 featureMatrix <- intensityMatrix(peaks, maldi_data)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	450 #elif str($centroids) == "TRUE"
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	451 featureMatrix <- intensityMatrix(peaks)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	452 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	453 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	454 featureMatrix2 =cbind(pixelnames, featureMatrix)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	455 colnames(featureMatrix2)[1] = c("mz")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	456 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	457 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	458 }else{print("There are no spectra with peaks left")}
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	459
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	460
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	461 #elif str( $method.methods_conditional.method ) == 'Filtering':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	462
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	463 print('filtering')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	464 ##m/z filtering
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	465
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	466 ## filtering on all pixels or on pixel groups:
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	467 #if str($method.methods_conditional.filter_annot_groups ) == 'FALSE':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	468
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	469 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	470 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	471 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	472 mergeWhitelists=$method.methods_conditional.mergeWhitelists)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	473
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	474 #elif str( $method.methods_conditional.filter_annot_groups ) == 'TRUE':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	475
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	476 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	477 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	478 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	479 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	480 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	481
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	482 ##QC plot and numbers
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	483 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	484 for (random_sample in random_spectra){
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	485 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	486 title("Filtered spectra", outer=TRUE, line=0)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	487 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	488 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	489 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	490 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	491 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	492 filtered = c(minmz, maxmz,number_features,mean_features, medint)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	493 QC_numbers= cbind(QC_numbers, filtered)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	494 vectorofactions = append(vectorofactions, "filtered")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	495
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	496 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	497 featureMatrix <- intensityMatrix(peaks)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	498 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	499 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	500 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	501 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	502 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	503 featureMatrix2 =cbind(pixelnames, featureMatrix)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	504 colnames(featureMatrix2)[1] = c("mz")
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	505 featureMatrix2 = t(featureMatrix2)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	506 }else{print("There are no spectra with peaks left")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	507 featureMatrix2 = matrix(0, ncol=1, nrow=1)}
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	508 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	509 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	510 #end for
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	511
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	512 if (length(peaks[!sapply(peaks, isEmpty)])>0){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	513 ## mass peaks output
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	514 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	515 for (spectrum in 1:length(peaks)){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	516 spectrum_df = data.frame(peaks[[spectrum]]@snr, peaks[[spectrum]]@mass, peaks[[spectrum]]@intensity)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	517 spectrum_df\$spectrum_id = rep(pixelnames[[spectrum]], length(peaks[[spectrum]]@mass))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	518 mass_peaks = rbind(mass_peaks,spectrum_df)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	519 }
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	520 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	521 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	522 }else{print("There are no spectra with peaks left")}
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	523
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	524 ## print table with QC values
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	525 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity")
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	526 plot(0,type='n',axes=FALSE,ann=FALSE)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	527 grid.table(t(QC_numbers))
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	528
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	529 dev.off()
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	530
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	531 if (summarized_spectra == FALSE){
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	532 #if $infile.ext == 'imzml'
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	533 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=TRUE)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	534 #elif $infile.ext == 'tabular'
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	535 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\_")), ncol=3, byrow=TRUE)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	536 ## extract x and y values and create the coordinate matrix in case tabular was input
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	537 peaklist_coordinates = unique(cbind(as.numeric(masspeaks_coordinates[,2]), as.numeric(masspeaks_coordinates[,3])))
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	538 exportImzMl(peaks, file="out.imzMl", processed=TRUE, coordinates=peaklist_coordinates)
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	539 #elif $infile.ext == 'rdata'
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	540 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=TRUE, coordinates=cardinal_coordinates)
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	541 #end if
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	542
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	543 }
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	544
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	545 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	546 </configfile>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	547 </configfiles>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	548 <inputs>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	549 <param name="infile" type="data" format="imzml,tabular,rdata" label="MSI data" help="Input file as imzML (composite upload), tabular peaklist or Cardinal MSImageSet saved as RData (regular upload)"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	550 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done. Peak detection cannot be run again on centroided data" truevalue="TRUE" falsevalue="FALSE"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	551 <conditional name="restriction_conditional">
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	552 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	553 <option value="no_restriction" selected="True">No, calculate on entire file</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	554 <option value="restrict">Yes, restrict to spectra of interest</option>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	555 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	556 <when value="restrict">
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	557 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	558 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	559 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	560 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	561 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	562 <when value="no_restriction"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	563 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	564
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	565 <conditional name="tabular_annotation">
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	566 <param name="load_annotation" type="select" label="Spectra annotations" help="Annotations can be used for group wise peak detection or filtering">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	567 <option value="no_annotation" selected="True">No</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	568 <option value="yes_annotation">Yes</option>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	569 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	570 <when value="yes_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	571 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	572 help="Tabular file with three columns: x values, y values and pixel annotations"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	573 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	574 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	575 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	576 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	577 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	578 <when value="no_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	579 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	580 <repeat name="methods" title="Method" min="1">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	581 <conditional name="methods_conditional">
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	582 <param name="method" type="select" label="Select a method">
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	583 <option value="Peak_detection">Peak detection</option>
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	584 <option value="monoisotopic_peaks">Monoisotopic peaks</option>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	585 <option value="Align">Align Spectra (warping/phase correction)</option>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	586 <option value="Binning">Binning</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	587 <option value="Filtering">Filtering</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	588 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	589 <when value="Peak_detection">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	590 <param name="peak_method" type="select" label="Noise estimation function">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	591 <option value="MAD" selected="True">MAD</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	592 <option value="SuperSmoother">SuperSmoother</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	593 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	594 <param name="halfWindowSize" type="integer" value="20"
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	595 label="Half window size (number of data points)"
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	596 help="The resulting window reaches from
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	597 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	598 (window size is 2*halfWindowSize+1).
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	599 The best size differs depending on the selected smoothing method."/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	600 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	601 <param name="use_annotations" type="boolean" label="Detect peaks on average mass spectra" help="Spectra with same annotation are averaged before peak detection, no imzML output" truevalue="TRUE" falsevalue="FALSE"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	602 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	603 <when value="monoisotopic_peaks">
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	604 <param name="minCor" type="float" value="0.95" label="Minimal correlation"
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	605 help="Minimal correlation between the peak pattern generated by the model and the experimental peaks in the MassPeaks object to be recognized as isotopic pattern."/>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	606 <param name="tolerance" type="float" label="Tolerance" value="0.0001"
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	607 help="Maximal relative deviation of a peak position (m/z) to be considered as identical: abs(((mass[i]+distance)-mass[i+1])/mass[i]) smaller than 'tolerance'. For 100ppm use 0.0001" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	608 <param name="distance" type="text" label="Distance" value="1.00235" help="Distance between two consecutive peaks in an isotopic pattern. 1.00235 is average distance for polypeptides. Multiple values can be used to find multiple charged pattern e.g. 1, 0.5 ,0.33">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	609 <sanitizer invalid_char="">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	610 <valid initial="string.digits">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	611 <add value="," />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	612 <add value=":" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	613 <add value="." />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	614 </valid>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	615 </sanitizer>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	616 </param>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	617 <param name="size" type="text" label="Size" value="3:10" help="Size (length) of isotopic pattern, longer patterns are prefered over shorter ones, min size is 2, a range can be used.">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	618 <sanitizer invalid_char="">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	619 <valid initial="string.digits">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	620 <add value=":" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	621 </valid>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	622 </sanitizer>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	623 </param>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	624 </when>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	625
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	626 <when value="Align">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	627 <param name="warping_method" type="select" label="Warping methods">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	628 <option value="lowess" selected="True">Lowess</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	629 <option value="linear">Linear</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	630 <option value="quadratic">Quadratic</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	631 <option value="cubic">Cubic</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	632 </param>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	633 <param name="tolerance" type="float" value="0.00005"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	634 label="Tolerance = abs(mz1 - mz2)/mz2"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	635 help="Maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" />
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	636 <param name="allow_nomatch" type="boolean" label="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	637 <param name="empty_nomatch" type="boolean" label="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	638 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	639
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	640 <conditional name="reference_for_alignment">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	641 <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">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	642 <option value="no_reference" selected="True">no reference</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	643 <option value="yes_reference">reference from tabular file</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	644 </param>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	645 <when value="no_reference">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	646 <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"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	647 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	648 <when value="yes_reference">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	649 <param name="reference_file" type="data" format="tabular"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	650 label="Reference m/z values"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	651 help="Tabular file"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	652 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	653 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	654 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	655 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	656 </conditional>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	657 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	658
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	659 <when value="Binning">
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	660 <param name="bin_tolerance" type="float" value="0.002" label="Tolerance"
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	661 help="After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical."/>
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	662 <param name="bin_method" display="radio" type="select" label="Bin creation rule" help="strict - creates bins never containing two or more peaks of the same sample. relaxed - allows multiple peaks of the same sample in one bin.">
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	663 <option value="strict" selected="True" >strict</option>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	664 <option value="relaxed" >relaxed</option>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	665 </param>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	666 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	667 <when value="Filtering">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	668 <param name="minFrequency" type="float" value="0.25"
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	669 label="Removal of all peaks which occur in less than minFrequency spectra" help="Relative threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	670 <param name="minNumber" type="float" value="1.0"
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	671 label="Removal of all peaks which occur in less than minNumber spectra" help="Absolute threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	672 <param name="filter_annot_groups" type="boolean" label="Group wise filtering with pixel annotations." help="If not specified a single group is assumed or when filtering has been done group wise it will automatically be group wise when selecting filtering on all pixel" truevalue="TRUE" falsevalue="FALSE"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	673 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	674 label="mergeWhitelists" help="Yes means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	675 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	676 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	677 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	678 </inputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	679 <outputs>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	680 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzml">
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	681 <!--filter>methods_conditional['method'] == 'Peak_detection'</filter-->
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	682 </data>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	683 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "${tool.name} on ${on_string}: QC"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	684 <data format="tabular" name="masspeaks" label="${tool.name} on ${on_string}: peaklist"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	685 <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	686 </outputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	687 <tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	688 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	689 <param name="infile" value="" ftype="imzml">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	690 <composite_data value="Example_Continuous.imzML"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	691 <composite_data value="Example_Continuous.ibd"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	692 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	693 <conditional name="tabular_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	694 <param name="load_annotation" value="yes_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	695 <param name="annotation_file" value="pixel_annotations.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	696 <param name="column_x" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	697 <param name="column_y" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	698 <param name="column_names" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	699 <param name="tabular_header" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	700 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	701 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	702 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	703 <param name="method" value="Peak_detection"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	704 <param name="peak_method" value="SuperSmoother"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	705 <param name="halfWindowSize" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	706 <param name="snr" value="5"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	707 <param name="use_annotations" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	708 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	709 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	710 <output name="plots" file="peakdetection1_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	711 <output name="masspeaks" file="masspeaks1.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	712 <output name="intensity_matrix" file="int1.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	713 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	714 <test>
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	715 <param name="infile" value="masspeaks3_forinput.tabular"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	716 <param name="centroids" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	717 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	718 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	719 <param name="method" value="monoisotopic_peaks"/>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	720 <param name="tolerance" value="0.0004"/>
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	721 <param name="size" value="3"/>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	722 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	723 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	724 <output name="plots" file="peakdetection2_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	725 <output name="masspeaks" file="masspeaks2.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	726 <output name="intensity_matrix" file="int2.tabular"/>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	727 <output name="outfile_imzml" ftype="imzml" file="peak_detection2.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	728 <extra_files type="file" file="peak_detection2.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	729 <extra_files type="file" file="peak_detection2.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	730 </output>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	731 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	732 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	733 <param name="infile" value="" ftype="imzml">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	734 <composite_data value="Example_Continuous.imzML"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	735 <composite_data value="Example_Continuous.ibd"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	736 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	737 <conditional name="tabular_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	738 <param name="load_annotation" value="yes_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	739 <param name="annotation_file" value="pixel_annotations.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	740 <param name="column_x" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	741 <param name="column_y" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	742 <param name="column_names" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	743 <param name="tabular_header" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	744 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	745 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	746 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	747 <param name="method" value="Peak_detection"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	748 <param name="peak_method" value="MAD"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	749 <param name="halfWindowSize" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	750 <param name="snr" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	751 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	752 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	753 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	754 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	755 <param name="method" value="Binning"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	756 <param name="bin_tolerance" value="0.01"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	757 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	758 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	759 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	760 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	761 <param name="method" value="Filtering"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	762 <param name="minFrequency" value="0.5"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	763 <param name="minNumber" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	764 <param name="filter_annot_groups" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	765 <param name="mergeWhitelists" value="FALSE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	766 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	767 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	768 <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	769 <output name="intensity_matrix" file="intensity_matrix3.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	770 <output name="masspeaks" file="masspeaks3.tabular"/>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	771 <output name="outfile_imzml" ftype="imzml" file="peak_detection3.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	772 <extra_files type="file" file="peak_detection3.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	773 <extra_files type="file" file="peak_detection3.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	774 </output>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	775 </test>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	776 <test>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	777 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	778 <param name="method" value="Peak_detection"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	779 <param name="peak_method" value="MAD"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	780 <param name="halfWindowSize" value="20"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	781 <param name="snr" value="2"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	782 <output name="plots" file="peakdetection4_QC.pdf" compare="sim_size"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	783 <output name="intensity_matrix" file="intensity_matrix4.tabular"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	784 <output name="masspeaks" file="masspeaks4.tabular"/>
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	785 <output name="outfile_imzml" ftype="imzml" file="peak_detection4.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	786 <extra_files type="file" file="peak_detection4.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	787 <extra_files type="file" file="peak_detection4.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	788 </output>
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	789 </test>
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	790 </tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	791 <help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	792 <![CDATA[
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	793
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	794 @MADLI_QUANT_DESCRIPTION@
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	795
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	796 -----
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	797
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	798 Input data
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	799
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	800 - MSI data: 3 types of input data can be used:
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	801
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	802 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	803 - Cardinal "MSImageSet" data saved as .RData
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	804 - MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". The spectrum has to be in the following format: xy_1_1 (for pixel coordinates x1y1). The header must have exactly the four column names.
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	805
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	806 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	807
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	808 snr mass intensity spectrum
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	809 5.34 304.16 0.10 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	810 12.09 305 0.2 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	811 6.80 306.25 0.133 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	812 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	813 ...
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	814
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	815
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	816 - 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.
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	817
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	818 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	819
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	820 x_coord y_coord
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	821 1 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	822 2 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	823 3 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	824 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	825 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	826
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	827
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	828 - Optional: Tabular file(s) containing pixel coordinates and annotation. X and y values in separate columns and the corresponding annotation in a third column. Tabular files with any header name or no header at all are supported. The annotations can be used to either detect peak on the average mass spectrum of each annotation group ('Detect peaks on average mass spectra') or to filter for peaks within pixel groups ('Group wise filtering'). This option is not compatible with tabular peak list inputs.
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	829
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	830 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	831
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	832 x_coord y_coord annotation
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	833 1 1 healthy
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	834 2 1 healthy
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	835 3 1 disease
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	836 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	837 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	838
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	839 Options
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	840
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	841 - Peak detection: detection of peaks, only possible with profile mode input. A peak is a local maximum above a user defined noise threshold.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	842
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	843 - Two functions exist to estimate the noise: MAD and supersmoother.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	844 - SNR is an abbreviation for signal-to-noise-ratio. A local maximum has to be higher than SNR*noise to be recognize as peak.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	845 - 'halfWindowSize': The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum has to be the highest one in the given window to be recognized as peak.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	846 - Detect peaks on average mass spectra: Spectra with the same annotation (taken from the annotation tabular input) are averaged and peak picking is performed on the average spectrum of each annotation group. The exported imzML is empty and cannot be used for further analysis steps. The peaklist and intensity matrix outputs contain the annotation group names with their averaged intensity values. Filtering steps have to be done in the same run as the peak picking.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	847
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	848
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	849 - Monoisotopic peaks: Keeps only the monoisotopic peaks
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	850
4 c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	851 - Based on poisson model for isotopic patterns as decribed in (`Breen et al. <https://doi.org/10.1002/1522-2683(20000601)21:11%3C2243::AID-ELPS2243%3E3.0.CO;2-K>`_)
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	852 - Isotopic pattern can be characterized and recognized by
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	853
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	854 - the similarity of the experimental pattern with the modelled pattern
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	855 - the distance between consecutive isotopic peaks. For polypeptides the average distance is 1.00235 (`Park et al. <https://pubs.acs.org/doi/abs/10.1021/ac800913b>`_). Multiply charged analytes have smaller distances between the peaks (e.g. z = 1 distance = ~1; z = 2: distance = ~0.5; z = 3: distance = ~0.3333) To search for differently charged isotopic pattern multiple distances can be applied - the order matters because the first distance that matches is reported (1, 0.5, 0.3333).
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	856 - the size (length) of the pattern, multiple values can be applied, longer patterns are prefered over shorter ones.
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	857
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	858
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	859 - Spectra alignment (warping): alignment for (re)calibration of m/z values.
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	860
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	861 - without external reference m/z: internal reference is obtained by filtering (default 90%) and binning the peaks to find landmark peaks and their average m/z
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	862 - with external reference m/z: the m/z provided in a tabular file are used as a reference, at least 10 reference values are recommended
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	863 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. This requirement can be skipped by setting "Don't throw an error when less than 2 reference m/z were found in a spectrum" 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.
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	864
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	865
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	866 - Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical. The algorithm is based on the following workflow:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	867
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	868 1. Put all m/z in a sorted vector.
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	869 2. Calculate differences between each neighbor.
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	870 3. Divide the m/z vector at the largest gap (largest difference) and form a left and a right bin.
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	871 4. Rerun step 3 for the left and/or the right bin if they don't fulfill the following criteria:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	872
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	873 - All peaks in a bin are near to the mean (abs(mass-meanMass)/meanMass < tolerance).
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	874 - method == "strict": The bin doesn't contain two or more peaks of the same sample.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	875
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	876
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	877 - Peak filtering: Removal of less frequent m/z features:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	878
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	879 - minFrequency : between 0 and 1: m/z has to occur in 0 - 100% of all spectra; minNumber: m/z has to occur in at least this amount of spectra --> out of those two criteria the stricter value will be used
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	880 - Group wise filtering with pixel annotations: 'Yes' means that the filtering criteria are applied for each annotation group separately.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	881 - mergeWhitelists: 'Yes' means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	882 - To filter data that was averaged before peak detection: Filtering has to be done in the same tool run as the peak detection. The filtering criteria are automatically applied per annotation group (Group wise filtering can be 'No') and not per pixel. Example: to keep only m/z that were detected in at least half of all annotation groups set minFrequency to 0.5.
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	883
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	884
1 96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: 0 diff changeset	885 Output
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	886
3 c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	887 - centroided, processed imzML file, imzML file is empty when 'Detect peaks on average mass spectra' is chosen.
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 2 diff changeset	888 - pdf with mass spectra plots of four random spectra and a table with key values after each preprocessing step
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	889 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
2 41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 1 diff changeset	890 - tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. For peak picking on the average of multiple spectra, each spectra group is a column with mean intensities for each m/z.
0 3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	891
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	892 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	893
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	894 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	895 </help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	896 <expand macro="citation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 galaxyp parents: diff changeset	897 </tool>

Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate maldi_quant_peakdetection.xml @ 5:af766257766e draft