cardinal_preprocessing: preprocessing.xml annotate

annotate preprocessing.xml @ 18:83aac7741200 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c

author	galaxyp
date	Thu, 04 Jul 2024 13:38:14 +0000
parents	611d80c0e29d
children

rev	line source
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	2 <description>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	3 mass spectrometry imaging preprocessing
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	4 </description>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	5 <macros>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	6 <import>macros.xml</import>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	7 </macros>
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	8 <expand macro="requirements"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	9 <command detect_errors="exit_code">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	10 <![CDATA[
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	11
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	12 @INPUT_LINKING@
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	13 cat '${cardinal_preprocessing}' &&
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	14 Rscript '${cardinal_preprocessing}' &&
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	15
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	16 mkdir $outfile_imzml.files_path &&
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	17 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" \| true &&
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	18 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" \| true &&
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	19 echo "imzML file:" > $outfile_imzml &&
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	20 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	21
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	22 ]]>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	23 </command>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	24 <configfiles>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	25 <configfile name="cardinal_preprocessing"><![CDATA[
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	26
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	27 ################################# load libraries and read file #################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	28
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	29 ## set CPU, default = 1
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	30
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	31 if (Sys.getenv("GALAXY_SLOTS")!="")
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	32 {
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	33 number_cpu = 1 ## default = 1
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	34 }else{
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	35 number_cpu = as.numeric(Sys.getenv("GALAXY_SLOTS")) ##cpu set by Galaxy
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	36 }
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	37
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	38 library(Cardinal)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	39 library(gridExtra)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	40 library(ggplot2)
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	41 library(sva)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	42 library(randomcoloR)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	43
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	44
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	45 @READING_MSIDATA_FULLY_COMPATIBLE@
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	46
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	47
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	48 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	49
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	50 ## set variable to False
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	51 #set $used_peak_picking = False
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	52 #set $used_peak_alignment = False
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	53 #set $continuous_format = False
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	54
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	55
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	56 if (ncol(msidata)>0 & nrow(msidata) >0){
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	57
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	58 ## start QC report
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	59
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	60 pdf("Preprocessing.pdf", fonts = "Times", pointsize = 12)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	61 plot(0,type='n',axes=FALSE,ann=FALSE)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	62 title(main=paste("Quality control during preprocessing \n", "Filename:", "$infile.display_name"))
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	63
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	64 ######################### preparations for QC report #################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	65
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	66 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	67 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	68 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	69 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	70 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, pixelcount))
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	71 vectorofactions = "inputdata"
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	72 ## Choose random spectra for QC plots
f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	73 random_spectra = sample(pixels(msidata), 4, replace=FALSE)
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	74 par(oma=c(0,0,2,0))
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	75 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	76 title("Input spectra", outer=TRUE, line=0)
f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	77
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	78 ############################### Preprocessing steps ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	79 ###############################################################################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	80
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	81 #for $method in $methods:
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	82
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	83 ############################### Normalization ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	84
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	85 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	86 print('Normalization')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	87 ##normalization
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	88
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	89 msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	90 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	91
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	92
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	93 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	94
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	95 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	96 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	97 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	98 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	99 normalized = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	100 QC_numbers= cbind(QC_numbers, normalized)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	101 vectorofactions = append(vectorofactions, "normalized")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	102 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	103 title("Spectra after normalization", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	104
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	105 ############################### Baseline reduction ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	106
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	107 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	108 print('Baseline_reduction')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	109 ##baseline reduction
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	110
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	111 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	112 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	113
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	114 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	115
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	116 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	117 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	118 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	119 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	120 baseline = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	121 QC_numbers= cbind(QC_numbers, baseline)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	122 vectorofactions = append(vectorofactions, "baseline red.")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	123 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	124 title("Spectra after baseline reduction", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	125
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	126 ############################### Smoothing ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	127
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	128 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	129 print('Smoothing')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	130 ## Smoothing
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	131
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	132 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	133 print('gaussian smoothing')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	134
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	135 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	136 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	137
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	138 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	139 print('sgolay smoothing')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	140
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	141 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	142 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	143
141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	144 ## if selected replace negative intensities with zero
141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	145 #if $method.methods_conditional.methods_for_smoothing.replace_negatives:
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	146 ## bring spectra matrix to disk
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	147 spectra_df = as.matrix(spectra(msidata))
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	148 spectra_df[spectra_df<0] = 0
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	149 spectra(msidata) = spectra_df
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	150 #end if
141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	151
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	152 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	153 print('moving average smoothing')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	154
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	155 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	156 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	157
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	158 #end if
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	159
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	160 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	161
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	162 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	163 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	164 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	165 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	166 smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	167 QC_numbers= cbind(QC_numbers, smoothed)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	168 vectorofactions = append(vectorofactions, "smoothed")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	169 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	170 title("Spectra after smoothing", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	171
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	172
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	173 ############################### Mz alignment ###########################
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	174
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	175 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment':
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	176 print('m/z alignment')
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	177 ## M/z alignment
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	178
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	179 #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table':
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	180
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	181 reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	182 reference_mz = reference_mz[,$method.methods_conditional.mzalign_ref_type.feature_column]
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	183
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	184 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	185
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	186
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	187 #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref':
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	188
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	189 msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	190
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	191 #end if
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	192
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	193 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	194
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	195 ############################### QC ###########################
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	196
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	197 maxfeatures =nrow(msidata)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	198 pixelcount = ncol(msidata)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	199 minmz = round(min(mz(msidata)), digits=2)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	200 maxmz = round(max(mz(msidata)), digits=2)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	201 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	202 QC_numbers= cbind(QC_numbers, mz_aligned)
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	203 vectorofactions = append(vectorofactions, "mz aligned")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	204 print(plot(msidata, pixel=random_spectra, col="black"))
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	205 title("Spectra after m/z alignment", outer=TRUE, line=0)
15 accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	206
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	207
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	208 ############################### Mz recalibration ###########################
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	209
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	210 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_recalibration':
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	211 print('m/z recalibration')
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	212 ## M/z recalibration
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	213
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	214 reference_mz = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	215 reference_mz = reference_mz[,$method.methods_conditional.feature_column]
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	216
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	217 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	218
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	219 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	220
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	221 ## remove the reference peaks data to allow proper peak alignment afterwards
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	222 metadata(featureData(msidata))['reference peaks'] <- NULL
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	223
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	224 ############################### QC ###########################
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	225
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	226 maxfeatures =nrow(msidata)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	227 pixelcount = ncol(msidata)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	228 minmz = round(min(mz(msidata)), digits=2)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	229 maxmz = round(max(mz(msidata)), digits=2)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	230 mz_recal = c(minmz, maxmz,maxfeatures, pixelcount)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	231 QC_numbers= cbind(QC_numbers, mz_recal)
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	232 vectorofactions = append(vectorofactions, "mz recalibrated")
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	233 print(plot(msidata, pixel=random_spectra, col="black"))
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	234 title("Spectra after m/z recalibration", outer=TRUE, line=0)
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	235
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	236
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	237 ############################### Peak picking ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	238
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	239 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	240 #set $used_peak_picking = True
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	241 print('Peak_picking')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	242 ## Peakpicking
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	243
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	244 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	245 print('adaptive peakpicking')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	246
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	247 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	248
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	249 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'mad':
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	250 print('mad peakpicking')
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	251
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	252 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	253
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	254 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	255 print('simple peakpicking')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	256
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	257 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	258
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	259 #end if
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	260 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	261
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	262
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	263 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	264
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	265 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	266 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	267 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	268 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	269 picked = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	270 QC_numbers= cbind(QC_numbers, picked)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	271 vectorofactions = append(vectorofactions, "picked")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	272 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	273 title("Spectra after peak picking", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	274
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	275 ############################### Peak alignment ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	276
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	277 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	278 #set $used_peak_alignment = True
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	279 print('Peak_alignment')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	280 ## Peakalignment
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	281
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	282 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	283
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	284 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.mz_tabular", header = $method.methods_conditional.align_ref_type.feature_header, stringsAsFactors = FALSE)
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	285
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	286 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.feature_column]
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	287
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	288 align_peak_reference = as.numeric(align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))])
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	289 if (length(align_peak_reference) == 0)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	290 {align_peak_reference = 0}
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	291
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	292 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment", ref=align_peak_reference)
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	293
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	294
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	295 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	296
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	297 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment")
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	298
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	299 #end if
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	300
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	301 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	302
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	303
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	304 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	305
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	306 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	307 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	308 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	309 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	310 aligned = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	311 QC_numbers= cbind(QC_numbers, aligned)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	312 vectorofactions = append(vectorofactions, "aligned")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	313 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	314 title("Spectra after alignment", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	315
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	316 ############################### Peak filtering ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	317
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	318 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	319 print('Peak_filtering')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	320
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	321 msidata = peakFilter(msidata, freq.min = $method.methods_conditional.frequ_filtering)
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	322 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	323
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	324 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	325
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	326 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	327 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	328 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	329 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	330 filtered = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	331 QC_numbers= cbind(QC_numbers, filtered)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	332 vectorofactions = append(vectorofactions, "filtered")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	333 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	334 title("Spectra after filtering", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	335
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	336 ############################### Peak binning ###########################
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	337
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	338 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_binning':
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	339 print('Peak_binning')
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	340
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	341 ## reading reference file
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	342 reference_table = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	343 reference_column = reference_table[,$method.methods_conditional.feature_column]
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	344 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	345
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	346 msidata = peakBin(msidata, ref = peak_reference, tolerance = $method.methods_conditional.peakbin_tol, units = "$method.methods_conditional.peakbin_units", type="$method.methods_conditional.peaks_type")
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	347 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	348
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	349 ############################### QC ###########################
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	350
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	351 maxfeatures =nrow(msidata)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	352 pixelcount = ncol(msidata)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	353 minmz = round(min(mz(msidata)), digits=2)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	354 maxmz = round(max(mz(msidata)), digits=2)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	355 peak_binned = c(minmz, maxmz,maxfeatures, pixelcount)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	356 QC_numbers= cbind(QC_numbers, peak_binned)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	357 vectorofactions = append(vectorofactions, "peak binned")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	358 print(plot(msidata, pixel=random_spectra, col="black"))
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	359 title("Spectra after peak binning", outer=TRUE, line=0)
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	360
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	361
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	362 ############################### Mass binning ###########################
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	363
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	364 #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning':
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	365 print('mass binning')
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	366
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	367 #if str($method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	368
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	369 msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	370
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	371
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	372 #elif str($method.methods_conditional.mz_range.features_filtering) == 'none':
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	373
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	374 msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	375
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	376 #elif str($method.methods_conditional.mz_range.features_filtering) == 'bin_to_reference':
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	377
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	378 bin_reference_mz = read.delim("$method.methods_conditional.mz_range.mz_tabular", header = $method.methods_conditional.mz_range.feature_header, stringsAsFactors = FALSE)
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	379 bin_reference_mz = bin_reference_mz[,$method.methods_conditional.mz_range.feature_column]
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	380
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	381 msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun",
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	382 ref=bin_reference_mz)
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	383
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	384 #end if
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	385
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	386 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	387
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	388 ## optional: replace NA with 0
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	389 #if $method.methods_conditional.replace_NA_bin:
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	390 ## count and replace NAs
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	391 print(paste0("Number of NA that were set to zero after binning:",sum(is.na(spectra(msidata)))))
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	392 spectra(msidata)[is.na(spectra(msidata))] = 0
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	393 #end if
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	394
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	395 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	396
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	397 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	398 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	399 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	400 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	401 reduced = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	402 QC_numbers= cbind(QC_numbers, reduced)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	403 vectorofactions = append(vectorofactions, "reduced")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	404 print(plot(msidata, pixel=random_spectra, col="black"))
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	405 title("Spectra after m/z binning", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	406
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	407 ############################### Transformation ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	408
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	409 #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	410 print('Transformation')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	411
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	412 if (class(msidata) == "MSProcessedImagingExperiment"){
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	413 msidata = as(msidata, "MSContinuousImagingExperiment")
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	414 }
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	415
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	416 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	417 print('log2 transformation')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	418
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	419 ## replace 0 with NA to prevent Inf
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	420 spectra_df = as.matrix(spectra(msidata)) ## convert into R matrix
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	421 spectra_df[spectra_df ==0] = NA
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	422 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df))))
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	423 spectra(msidata) = spectra_df
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	424 ## log transformation
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	425 spectra(msidata) = log2(spectra(msidata))
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	426 ## optional: replace NA with 0
1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	427 #if $method.methods_conditional.transf_conditional.replace_NA_trans:
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	428 spectra(msidata)[is.na(spectra(msidata))] = 0
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	429 #end if
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	430
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	431 #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt':
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	432 print('squareroot transformation')
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	433
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	434 spectra(msidata) = sqrt(spectra(msidata))
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	435
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	436 #end if
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	437
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	438 ############################### QC ###########################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	439
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	440 maxfeatures =nrow(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	441 pixelcount = ncol(msidata)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	442 minmz = round(min(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	443 maxmz = round(max(mz(msidata)), digits=2)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	444 transformed = c(minmz, maxmz,maxfeatures, pixelcount)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	445 QC_numbers= cbind(QC_numbers, transformed)
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	446 vectorofactions = append(vectorofactions, "transformed")
10 5abc3ab4792c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" galaxyp parents: 9 diff changeset	447 print(plot(msidata, pixel=random_spectra, col="black"))
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	448 title("Spectra after transformation", outer=TRUE, line=0)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	449
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	450
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	451
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	452
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	453 ############################### ComBat batch correction ###########################
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	454
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	455 #elif str( $method.methods_conditional.preprocessing_method) == 'ComBat_batch_correction':
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	456 print('ComBat batch correction of centroided data')
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	457
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	458 ## load annotation tabular and define batch and condition column
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	459 annotation = read.delim("$method.methods_conditional.annotation_file", header=$method.methods_conditional.feature_header, sep="\t")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	460 annotation_x = annotation[,$method.methods_conditional.x_column]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	461 annotation_y = annotation[,$method.methods_conditional.y_column]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	462 batch = annotation[,$method.methods_conditional.batch_column]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	463 condition = annotation[,$method.methods_conditional.condition_column]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	464
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	465 ### stop if not enough batches provided
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	466 tryCatch(
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	467 {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	468
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	469 if (unique(batch<2))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	470 {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	471 stop(call.=FALSE)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	472 }
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	473 },
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	474 error=function(cond) {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	475 ## in case user provided an annotation tabular with less than two batches
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	476 message("Error in annotation tabular")
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	477 message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary")
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	478 stop(call.=FALSE)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	479 }
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	480 )
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	481
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	482 ## get intensity matrix from imzml file
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	483 intensity_matrix = as.matrix(iData(msidata))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	484 mz_names = paste0("mz_", mz(msidata))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	485 pixel_names = paste0("xy_", msidata@elementMetadata@coord@listData[["x"]], "_", msidata@elementMetadata@coord@listData[["y"]])
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	486 rownames(intensity_matrix) = mz_names
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	487 colnames(intensity_matrix) = pixel_names
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	488
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	489 ## reorder columns of intensity matrix to row order of batch column
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	490 rownames(annotation) = paste0("xy_", annotation_x, "_", annotation_y)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	491 col_order = rownames(annotation)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	492
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	493 ### stop if pixel/sample names (columns) in intensity matrix from imzml file don't match samples names (rows) in annotation tabular file
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	494 tryCatch(
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	495 {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	496
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	497 if (all(colnames(intensity_matrix) %in% col_order == FALSE))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	498 {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	499 stop(call.=FALSE)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	500 }
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	501 },
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	502 error=function(cond) {
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	503 ## in case pixel names (columns) from the imzml file don't match the pixel names in the annotation tabular file
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	504 message("Error in annotation tabular")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	505 message("Possible problems: Annotation tabular file does not contain the correct pixel names (columns) from the imzml file)")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	506 stop(call.=FALSE)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	507 }
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	508 )
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	509
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	510 intensity_matrix = intensity_matrix[, col_order]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	511 print("columns have been ordered to annotation row order")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	512
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	513 ## execution of ComBat algorithm from sva package
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	514 combat_data = ComBat(dat = intensity_matrix, batch = batch, mod = NULL, par.prior = TRUE, prior.plots = FALSE)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	515 print("Combat has been executed")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	516
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	517 ## change intensity data of loaded imzml file after combat has been performed
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	518 iData(msidata) = as.matrix(combat_data)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	519
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	520 ############################### QC ###########################
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	521
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	522 maxfeatures =nrow(msidata)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	523 pixelcount = ncol(msidata)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	524 minmz = round(min(mz(msidata)), digits=2)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	525 maxmz = round(max(mz(msidata)), digits=2)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	526 batch_corrected = c(minmz, maxmz, maxfeatures, pixelcount)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	527 QC_numbers= cbind(QC_numbers, batch_corrected)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	528 vectorofactions = append(vectorofactions, "batch_corrected")
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	529 print(plot(msidata, pixel=random_spectra, col="black"))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	530 title("Spectra after ComBat batch correction", outer=TRUE, line=0)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	531
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	532
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	533 ## PCA plot function and execution
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	534 combat_data = as.data.frame(combat_data)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	535 intensity_data = as.data.frame(intensity_matrix)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	536
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	537 ## PCA function
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	538 plot_PCA = function(input_data, condition, batch, title, color){
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	539 data <- input_data
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	540 pca_data <- prcomp(t(data[, seq_len(ncol(input_data))]))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	541 pca_sdev <- pca_data[["sdev"]]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	542 pca_data_perc <- round(100 * pca_sdev^2 / sum(pca_sdev^2), 1)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	543 pca_components <- pca_data[["x"]]
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	544 df_pca_data <- data.frame(PC1 = pca_components[, 1], PC2 = pca_components[, 2], sample = colnames(input_data), condition = condition)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	545 ggplot(df_pca_data, aes(PC1, PC2, color = as.factor(batch), shape = as.factor(condition))) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	546 ggtitle(title) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	547 geom_point(size = 4) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	548 stat_ellipse(aes(PC1, PC2, color = as.factor(batch), group = as.factor(batch)), type = "norm")+
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	549 scale_color_manual(values=color) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	550 theme_bw() +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	551 theme(legend.position = "bottom", legend.box="vertical", plot.title = element_text(size = 12, hjust = 0.5), axis.title = element_text(size = 12), axis.text = element_text(size = 12, color = "black")) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	552 labs(x=paste0("PC1 (",pca_data_perc[1],")"), y=paste0("PC2 (",pca_data_perc[2],")")) +
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	553 labs(color = "Batches", shape = "Conditions")}
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	554
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	555 ## define colors
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	556 color_pal = distinctColorPalette(length(levels(as.factor(batch))))
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	557
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	558 ## execution of PCA plots
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	559 PCA_bc = plot_PCA(intensity_data, condition, batch, "before batch correction", color_pal)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	560 PCA_ac = plot_PCA(combat_data, condition, batch, "batch corrected", color_pal)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	561 print(PCA_bc)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	562 print(PCA_ac)
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	563
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	564 #end if
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	565 #end for
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	566
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	567 ############# Outputs: RData, imzml and QC report #############
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	568 ################################################################################
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	569
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	570 ## save msidata as imzML file, will only work if there is at least 1 m/z left
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	571
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	572 if (nrow(msidata) > 0){
3 f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	573 ## make sure that coordinates are integers
f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	574 coord(msidata)\$y = as.integer(coord(msidata)\$y)
f172efe92629 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	575 coord(msidata)\$x = as.integer(coord(msidata)\$x)
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	576 ## only continuous files can currently be exported
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	577 msidata = as(msidata, "MSContinuousImagingExperiment")
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	578 writeImzML(msidata, "out")
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	579 }
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	580
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	581 plot(0,type='n',axes=FALSE,ann=FALSE)
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	582 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "# spectra")
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	583 grid.table(t(QC_numbers))
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	584 dev.off()
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	585
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	586 }else{
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	587 print("inputfile has no intensities > 0")
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	588 }
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	589
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	590 ]]></configfile>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	591 </configfiles>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	592 <inputs>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	593 <expand macro="reading_msidata"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	594 <repeat name="methods" title="Preprocessing" min="1" max="50">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	595 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	596 <param name="preprocessing_method" type="select" label="Preprocessing methods">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	597 <option value="Normalization" selected="True">Intensity Normalization</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	598 <option value="Baseline_reduction">Baseline Reduction</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	599 <option value="Smoothing">Peak smoothing</option>
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	600 <option value="mz_alignment">m/z alignment</option>
15 accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	601 <option value="mz_recalibration">m/z recalibration</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	602 <option value="Peak_picking">Peak picking</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	603 <option value="Peak_alignment">Peak alignment</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	604 <option value="Peak_filtering">Peak filtering</option>
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	605 <option value="Peak_binning">Peak binning to reference peaks</option>
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	606 <option value="Mass_binning">m/z binning</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	607 <option value="Transformation">Transformation</option>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	608 <option value="ComBat_batch_correction">ComBat batch correction of centroided data</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	609 </param>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	610 <when value="Normalization">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	611 <conditional name="methods_for_normalization">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	612 <param name="normalization_method" type="select" label="Normalization method">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	613 <option value="tic" selected="True">TIC</option>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	614 <option value="rms">RMS</option>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	615 </param>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	616 <when value="tic"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	617 <when value="rms"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	618 </conditional>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	619 </when>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	620 <when value="Baseline_reduction">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	621 <param name="blocks_baseline" type="integer" value="500"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	622 label="Blocks"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	623 <param name="spar_baseline" type="float" value="1.0" label="Spar value"
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	624 help="Smoothing parameter for the spline smoothing
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	625 applied to the spectrum in order to decide the cutoffs
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	626 for throwing away false noise spikes that might occur inside peaks"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	627 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	628 <when value="Smoothing">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	629 <conditional name="methods_for_smoothing">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	630 <param name="smoothing_method" type="select" label="Smoothing method">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	631 <option value="gaussian" selected="True">gaussian</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	632 <option value="sgolay">Savitsky-Golay</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	633 <option value="ma">moving average</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	634 </param>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	635 <when value="gaussian">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	636 <param name="sd_gaussian" type="float" value="2"
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	637 label="The standard deviation for the Gaussian kernel. Default = window/4"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	638 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	639 <when value="sgolay">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	640 <param name="order_of_filters" type="integer" value="3"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	641 label="The order of the smoothing filter, must be smaller than window size"/>
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	642 <param name="replace_negatives" type="boolean" label="Replace negative intensities with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Savitzky golay smoothing can introduce negative intensity values it is recommended to replace them with zero"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	643 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	644 <when value="ma">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	645 <param name="coefficients_ma_filter" type="float" value="1"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	646 label="The coefficients for the moving average filter"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	647 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	648 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	649 <param name="window_smoothing" type="float" value="8"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	650 label="Window size"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	651 </when>
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	652 <when value="mz_alignment">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	653 <param name="alignment_tol" type="text" value="NA"
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	654 label="tolerance" help="The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	655 <sanitizer>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	656 <valid initial="string.digits">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	657 <add value="N" />
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	658 <add value="A" />
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	659 </valid>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	660 </sanitizer>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	661 </param>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	662 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	663 <option value="ppm" selected="True">ppm</option>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	664 <option value="mz">m/z</option>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	665 </param>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	666 <conditional name="mzalign_ref_type">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	667 <param name="align_reference_datatype" type="select" label="Choose reference">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	668 <option value="align_noref" selected="True">use mean spectrum as reference</option>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	669 <option value="align_table" >m/z values from tabular file as reference</option>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	670 </param>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	671 <when value="align_noref"/>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	672 <when value="align_table">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	673 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	674 </when>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	675 </conditional>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	676 <param name="quantile" type="float" value="0.2"
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	677 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	678 <param name="span" type="float" value="0.75"
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	679 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	680 </when>
15 accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	681 <when value="mz_recalibration">
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	682 <param name="alignment_tol" type="text" value="NA"
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	683 label="tolerance" help="The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.">
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	684 <sanitizer>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	685 <valid initial="string.digits">
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	686 <add value="N" />
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	687 <add value="A" />
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	688 </valid>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	689 </sanitizer>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	690 </param>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	691 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	692 <option value="ppm" selected="True">ppm</option>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	693 <option value="mz">m/z</option>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	694 </param>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	695 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	696 <param name="quantile" type="float" value="0.2"
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	697 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	698 <param name="span" type="float" value="0.75"
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	699 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	700 </when>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	701 <when value="Peak_picking">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	702 <param name="SNR_picking_method" type="float" value="6"
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	703 label="Signal to noise ratio"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	704 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	705 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	706 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	707 <param name="window_picking" type="float" value="5" label= "Window size" help="Window width for seeking local maxima"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	708 <conditional name="methods_for_picking">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	709 <param name="picking_method" type="select" label="Peak picking method">
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	710 <option value="adaptive" selected="True">adaptive</option>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	711 <option value="mad">mad</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	712 <option value="simple">simple</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	713 </param>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	714 <when value="adaptive">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	715 <param name="spar_picking" type="float" value="1.0"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	716 label="Spar value"
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	717 help = "Smoothing parameter for the spline smoothing
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	718 applied to the spectrum in order to decide the cutoffs
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	719 for throwing away false noise spikes that might occur inside peaks"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	720 </when>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	721 <when value="mad"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	722 <when value="simple"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	723 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	724 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	725 <when value="Peak_alignment">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	726 <param name="value_diffalignment" type="float" value="200"
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	727 label="tolerance" help="Peaks that differ less than this value will be aligned together"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	728 <param name="units_diffalignment" type="select" display="radio" optional="False" label="units">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	729 <option value="ppm" selected="True">ppm</option>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	730 <option value="mz">m/z</option>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	731 </param>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	732 <conditional name="align_ref_type">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	733 <param name="align_reference_datatype" type="select" label="Choose reference">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	734 <option value="align_noref" selected="True">no reference</option>
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	735 <option value="align_table" >m/z values from tabular file as reference</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	736 </param>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	737 <when value="align_noref"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	738 <when value="align_table">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	739 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	740 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	741 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	742 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	743 <when value="Peak_filtering">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	744 <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	745 </when>
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	746 <when value="Peak_binning">
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	747 <expand macro="reading_1_column_mz_tabular" label="A reference to which the peaks are binned." help="Tabular file with m/z features to extract from input file"/>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	748 <param name="peakbin_tol" value="NA" type="text" label="The tolerance to be used when matching the m/z features in the dataset to the reference. If this is NA, then automatically guess a resolution from the data." >
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	749 <sanitizer>
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	750 <valid initial="string.digits">
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	751 <add value="N" />
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	752 <add value="A" />
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	753 </valid>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	754 </sanitizer>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	755 </param>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	756 <param name="peakbin_units" display="radio" type="select" label="The units to use for the tolerance.">
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	757 <option value="mz" >mz</option>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	758 <option value="ppm" selected="True" >ppm</option>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	759 </param>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	760 <param name="peaks_type" type="select" display="radio"
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	761 label="Should the peak height or area under the curve be taken as the intensity value?">
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	762 <option value="height" selected="True">height</option>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	763 <option value="area">area</option>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	764 </param>
44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	765 </when>
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	766 <when value="Mass_binning">
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	767 <param name="bin_width" type="float" value="1" label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	768 <param name="bin_units" type="select" display="radio"
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	769 label="Unit for bin">
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	770 <option value="mz" selected="True">mz</option>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	771 <option value="ppm">ppm</option>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	772 </param>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	773 <param name="bin_fun" type="select" display="radio"
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	774 label="Calculate sum or mean intensity for ions of the same bin">
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	775 <option value="mean" selected="True">mean</option>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	776 <option value="sum">sum</option>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	777 </param>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	778 <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	779 <conditional name="mz_range">
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	780 <param name="features_filtering" type="select" label="Select m/z options">
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	781 <option value="none" selected="True">none</option>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	782 <option value="change_mz_range">change m/z range</option>
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	783 <option value="bin_to_reference">bin m/z to reference</option>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	784 </param>
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	785 <when value="none"/>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	786 <when value="change_mz_range">
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	787 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	788 <param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>
ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	789 </when>
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	790 <when value="bin_to_reference">
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	791 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features as reference for binning. Only the m/z values from the tabular file will be kept."/>
6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	792 </when>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	793 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	794 </when>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	795 <when value="Transformation">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	796 <conditional name="transf_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	797 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	798 <option value="log2" selected="True">log2</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	799 <option value="sqrt">sqrt</option>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	800 </param>
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	801 <when value="log2">
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	802 <param name="replace_NA_trans" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="0 values are set to NA before log2 transformation, after transformation they can be set back to 0"/>
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	803 </when>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	804 <when value="sqrt"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	805 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	806 </when>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	807 <when value="ComBat_batch_correction">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	808 <param name="annotation_file" type="data" format="tabular" label="Annotation file that contains the pixel x and y coordinates, the batch identifier, and the condition annotation for each spectrum." help="Annotation tabular file that contains the batch identifier for each spectrum in one column."/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	809 <param name="x_column" type="data_column" data_ref="annotation_file" label="X coordinates" help="Column with x coordinates of pixels."/>
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	810 <param name="y_column" type="data_column" data_ref="annotation_file" label="Y coordinates" help="Column with y coordinates of pixels."/>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	811 <param name="batch_column" type="data_column" data_ref="annotation_file" label="Batch column" help="The column that contains the batch identifier for each spectrum."/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	812 <param name="condition_column" type="data_column" data_ref="annotation_file" label="Condition column" help="The column that contains the condition annotation for each spectrum. Typically these are the groups you want to compare. If not applicable, the batch column can be selected again as this information is only used for the QC plot."/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	813 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	814 </when>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	815 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	816 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	817 </inputs>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	818 <outputs>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	819 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	820 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "${tool.name} on ${on_string}: QC"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	821 </outputs>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	822 <tests>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	823 <test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	824 <expand macro="infile_imzml"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	825 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	826 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	827 <param name="preprocessing_method" value="Normalization"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	828 <conditional name="methods_for_normalization">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	829 <param name="normalization_method" value="tic"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	830 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	831 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	832 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	833 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	834 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	835 <param name="preprocessing_method" value="Smoothing"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	836 <conditional name="methods_for_smoothing">
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	837 <param name="smoothing_method" value="sgolay"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	838 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	839 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	840 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	841 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	842 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	843 <param name="preprocessing_method" value="Peak_picking"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	844 <conditional name="methods_for_picking">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	845 <param name="picking_method" value="adaptive"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	846 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	847 <param name="blocks_picking" value="3"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	848 <param name="window_picking" value="3"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	849 <param name="SNR_picking_method" value="3"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	850 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	851 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	852 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	853 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	854 <param name="preprocessing_method" value="Peak_alignment"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	855 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	856 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	857 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	858 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	859 <param name="preprocessing_method" value="Peak_filtering"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	860 <param name="frequ_filtering" value="0.3"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	861 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	862 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	863 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	864 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	865 <param name="preprocessing_method" value="Transformation"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	866 <conditional name="transf_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	867 <param name="trans_type" value="sqrt"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	868 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	869 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	870 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	871 <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	872 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	873 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	874 <extra_files type="file" file="preprocessing_results1.ibd" name="ibd" compare="sim_size"/>
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	875 </output>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	876 </test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	877 <test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	878 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	879 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	880 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	881 <param name="preprocessing_method" value="Peak_picking"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	882 <param name="blocks_picking" value="3"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	883 <param name="window_picking" value="5"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	884 <param name="SNR_picking_method" value="2"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	885 <conditional name="methods_for_picking">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	886 <param name="picking_method" value="adaptive"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	887 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	888 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	889 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	890 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	891 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	892 <param name="preprocessing_method" value="Peak_alignment"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	893 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	894 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	895 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	896 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	897 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	898 <extra_files type="file" file="preprocessing_results2.ibd" name="ibd" compare="sim_size"/>
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	899 </output>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	900 </test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	901 <test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	902 <expand macro="infile_analyze75"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	903 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	904 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	905 <param name="preprocessing_method" value="Normalization"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	906 <conditional name="methods_for_normalization">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	907 <param name="normalization_method" value="rms"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	908 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	909 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	910 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	911 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	912 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	913 <param name="preprocessing_method" value="Peak_picking"/>
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	914 <param name="blocks_picking" value="20"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	915 <param name="window_picking" value="5"/>
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	916 <param name="SNR_picking_method" value="2"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	917 <conditional name="methods_for_picking">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	918 <param name="picking_method" value="mad"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	919 </conditional>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	920 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	921 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	922 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	923 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	924 <param name="preprocessing_method" value="Peak_alignment"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	925 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	926 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	927 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	928 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	929 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	930 <extra_files type="file" file="preprocessing_results3.ibd" name="ibd" compare="sim_size"/>
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	931 </output>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	932 </test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	933 <test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	934 <expand macro="infile_analyze75"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	935 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	936 <conditional name="methods_conditional">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	937 <param name="preprocessing_method" value="Normalization"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	938 <param name="normalization_method" value="tic"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	939 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	940 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	941 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	942 <conditional name="methods_conditional">
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	943 <param name="preprocessing_method" value="mz_alignment"/>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	944 </conditional>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	945 </repeat>
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	946 <repeat name="methods">
87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	947 <conditional name="methods_conditional">
15 accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	948 <param name="preprocessing_method" value="mz_recalibration"/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	949 <param name="alignment_tol" value="2"/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	950 <param name="alignment_units" value="ppm"/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	951 <param name="mz_tabular" value="inputcalibrantfile2.txt" ftype="tabular"/>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	952 <param name="feature_column" value="1"/>
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	953 <param name="feature_header" value="FALSE"/>
15 accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	954 </conditional>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	955 </repeat>
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	956 <repeat name="methods">
accf9fb6ea01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" galaxyp parents: 13 diff changeset	957 <conditional name="methods_conditional">
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	958 <param name="preprocessing_method" value="Mass_binning"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	959 <param name="bin_width" value="0.1"/>
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	960 <param name="bin_units" value="mz"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	961 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	962 </repeat>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	963 <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	964 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results4.imzml.txt" compare="sim_size">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	965 <extra_files type="file" file="preprocessing_results4.imzml" name="imzml" lines_diff="6"/>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	966 <extra_files type="file" file="preprocessing_results4.ibd" name="ibd" compare="sim_size"/>
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	967 </output>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	968 </test>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	969 <test>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	970 <expand macro="processed_infile_imzml"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	971 <conditional name="processed_cond">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	972 <param name="processed_file" value="processed"/>
9 ca727a6dede6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	973 <param name="accuracy" value="200"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	974 <param name="units" value="ppm"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	975 </conditional>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	976 <repeat name="methods">
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	977 <conditional name="methods_conditional">
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	978 <param name="preprocessing_method" value="Transformation"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	979 <conditional name="transf_conditional">
7 44a4b31fcbf3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 6 diff changeset	980 <param name="trans_type" value="log2"/>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	981 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	982 </conditional>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	983 </repeat>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	984 <repeat name="methods">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	985 <conditional name="methods_conditional">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	986 <param name="preprocessing_method" value="Baseline_reduction"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	987 </conditional>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	988 </repeat>
8 87bb011a4ee8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	989 <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size" delta="13000"/>
6 5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	990 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results5.imzml.txt" compare="sim_size">
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	991 <extra_files type="file" file="preprocessing_results5.imzml" name="imzml" lines_diff="6"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	992 <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/>
5bf056c0354e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" galaxyp parents: 5 diff changeset	993 </output>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	994 </test>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	995 <test>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	996 <param name="infile" value="" ftype="imzml">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	997 <composite_data value="Combat_40pixel.imzML" />
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	998 <composite_data value="Combat_40pixel.ibd"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	999 </param>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1000 <repeat name="methods">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1001 <conditional name="methods_conditional">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1002 <param name="preprocessing_method" value="ComBat_batch_correction"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1003 <param name="annotation_file" value="annotation_40pixel.tabular" ftype="tabular"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1004 <param name="feature_header" value="TRUE"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1005 <param name="x_column" value="2"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1006 <param name="y_column" value="3"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1007 <param name="batch_column" value="4"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1008 <param name="condition_column" value="6"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1009 </conditional>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1010 </repeat>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1011 <output name="QC_overview" file="preprocessing_results_combat_40pixel.pdf" compare="sim_size"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1012 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results_combat_40pixel.imzml.txt" compare="sim_size">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1013 <extra_files type="file" file="preprocessing_results_combat_40pixel.imzml" name="imzml" lines_diff="6"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1014 <extra_files type="file" file="preprocessing_results_combat_40pixel.ibd" name="ibd" compare="sim_size"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1015 </output>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1016 </test>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1017 <test>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1018 <expand macro="processed_infile_imzml"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1019 <conditional name="processed_cond">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1020 <param name="processed_file" value="processed"/>
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	1021 <param name="accuracy" value="200"/>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1022 <param name="units" value="ppm"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1023 </conditional>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1024 <repeat name="methods">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1025 <conditional name="methods_conditional">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1026 <param name="preprocessing_method" value="ComBat_batch_correction"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1027 <param name="annotation_file" value="Example_processed_ComBat_annotation.tabular" ftype="tabular"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1028 <param name="feature_header" value="TRUE"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1029 <param name="x_column" value="2"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1030 <param name="y_column" value="3"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1031 <param name="batch_column" value="4"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1032 <param name="condition_column" value="5"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1033 </conditional>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1034 </repeat>
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	1035 <output name="QC_overview" file="ComBat_results_Example_processed_file.pdf" compare="sim_size"/>
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1036 <output name="outfile_imzml" ftype="imzml" file="ComBat_results_Example_processed_file.imzml.txt" compare="sim_size">
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1037 <extra_files type="file" file="ComBat_results_Example_processed_file.imzml" name="imzml" lines_diff="6"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1038 <extra_files type="file" file="ComBat_results_Example_processed_file.ibd" name="ibd" compare="sim_size"/>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1039 </output>
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1040 </test>
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1041 </tests>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1042 <help>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1043 <![CDATA[
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1044
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1045 @CARDINAL_DESCRIPTION@
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1046
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1047 -----
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1048
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1049 This tool provides multiple Cardinal functions to preprocess mass spectrometry imaging data.
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1050
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1051 @MSIDATA_INPUT_DESCRIPTION@
1 1b22c1e7bfe7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	1052 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed after the data is read by the tool.
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1053 @MZ_TABULAR_INPUT_DESCRIPTION@
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1054
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1055 Options
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1056
12 e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1057 - Normalization: normalization of intensities to total ion current (TIC) or to root-mean-square (RMS)
e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1058 - Baseline reduction: baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets)
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1059 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection
12 e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1060 - m/z alignment: removes small m/z shifts between spectra
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1061 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1062 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1063 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot
12 e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1064 - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1065 - m/z binning: generates new m/z bins
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1066 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
18 83aac7741200 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c galaxyp parents: 17 diff changeset	1067 - ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally, a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:
17 611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1068
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1069 ::
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1070
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1071 x_coord y_coord batch_identifier condition
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1072 10 29 TMA_1 A
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1073 22 14 TMA_1 B
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1074 22 27 TMA_2 A
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1075 23 7 TMA_2 B
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1076 29 45 TMA_3 A
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1077 33 41 TMA_3 B
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1078 ...
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1079 ...
611d80c0e29d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 galaxyp parents: 15 diff changeset	1080
12 e0669b1854b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8" galaxyp parents: 11 diff changeset	1081
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1082
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1083 Output
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1084
13 6b36be80febb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" galaxyp parents: 12 diff changeset	1085 - MSI data as continuous imzML file
4 141a9288be9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1086 - pdf with key values and four random mass spectra after each processing step
0 8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1087
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1088 ]]>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1089 </help>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1090 <expand macro="citations"/>
8c05a34f160a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1091 </tool>
2 1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	1092

Mercurial > repos > galaxyp > cardinal_preprocessing

annotate preprocessing.xml @ 18:83aac7741200 draft default tip