Mercurial > repos > galaxyp > msi_filtering

annotate msi_filtering.xml @ 7:73b5a754f35c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 620a469e20836b921b6c0147421c8a4268b66ebd
author galaxyp
date Wed, 15 Aug 2018 05:40:01 -0400
parents bab12ded74a5
children 262db9893c6f
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73b5a754f35c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 620a469e20836b921b6c0147421c8a4268b66ebd
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1 <tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.5">
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2 <description>tool for filtering mass spectrometry imaging data</description>
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3 <requirements>
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4 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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5 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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6 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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11 #if $infile.ext == 'imzml'
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12 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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13 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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14 #elif $infile.ext == 'analyze75'
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15 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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16 ln -s '${infile.extra_files_path}/img' infile.img &&
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17 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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18 #else
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19 ln -s $infile infile.RData &&
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20 #end if
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21 cat '${MSI_subsetting}' &&
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22 echo ${MSI_subsetting} &&
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23 Rscript '${MSI_subsetting}'
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25 ]]>
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26 </command>
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27 <configfiles>
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28 <configfile name="MSI_subsetting"><![CDATA[
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31 ################################# load libraries and read file #################
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34 library(Cardinal)
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35 library(ggplot2)
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36 library(gridExtra)
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37
0
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38 #if $infile.ext == 'imzml'
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39 #if str($processed_cond.processed_file) == "processed":
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40 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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41 #else
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42 msidata <- readImzML('infile')
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43 #end if
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44 #elif $infile.ext == 'analyze75'
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45 msidata = readAnalyze('infile')
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46 #else
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47 load('infile.RData')
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48 #end if
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49
5
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51 ########################### QC numbers ########################
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52
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53 ## Number of features (m/z)
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54 maxfeatures = length(features(msidata))
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55 ## Range m/z
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56 minmz = round(min(mz(msidata)), digits=2)
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57 maxmz = round(max(mz(msidata)), digits=2)
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58 ## Number of spectra (pixels)
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59 pixelcount = length(pixels(msidata))
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60 ## Range x coordinates
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61 minimumx = min(coord(msidata)[,1])
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62 maximumx = max(coord(msidata)[,1])
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63 ## Range y coordinates
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64 minimumy = min(coord(msidata)[,2])
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65 maximumy = max(coord(msidata)[,2])
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66 ## Number of intensities > 0
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67 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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68 ## Spectra multiplied with m/z (potential number of peaks)
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69 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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70 ## Percentage of intensities > 0
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71 percpeaks = round(npeaks/numpeaks*100, digits=2)
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72 ## Number of empty TICs
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73 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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74 NumemptyTIC = sum(TICs == 0)
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75 ## median TIC
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76 medint = round(median(TICs), digits=2)
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77 ## Store features for QC plot
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78 featuresinfile = mz(msidata)
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79
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80 ## Next steps will only run if there are more than 0 intensities/pixels/features in the file
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82 if (sum(spectra(msidata)[]>0, na.rm=TRUE) > 0)
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83 {
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84
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85
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86 ## prepare dataframe for QC of pixel distribution (will be overwritten in filtering of pixels condition)
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87 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))
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88 colnames(position_df)[3] = "annotation"
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89
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90 ###################################### Filtering of pixels #####################
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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91 ################################################################################
0
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92
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93 #################### Pixels in the one column format "x=,y=" #####################
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94
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95 #if str($pixels_cond.pixel_filtering) == "single_column":
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96 print("single column")
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97
6
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98 ## read tabular file, count number of rows (= number of pixels), count how many pixels are valid
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99 input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE)
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100 startingrow = $pixels_cond.pixel_header+1
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101 numberpixels = length(startingrow:nrow(input_list))
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102 valid_entries = input_list[startingrow:nrow(input_list),$pixels_cond.pixel_column] %in% names(pixels(msidata))
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103 validpixels = sum(valid_entries)
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104 valid_annotations = input_list[valid_entries,c($pixels_cond.pixel_column, $pixels_cond.annotation_column)]
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105 colnames(valid_annotations) = c("pixel_coordinates", "annotation")
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106
6
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107 ## for valid pixels: filter file for pixels and create dataframe with x,y,annotation for QC
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108 if (validpixels != 0){
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109 ## filter file for pixels
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110 pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% valid_annotations[,1]]
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111 msidata = msidata[,pixelsofinterest]
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112 ## position_df for QC
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113
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114
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115 ###pixel_coords = coord(msidata)[names(pixels(msidata)) %in% valid_annotations[,1],1:2]
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116 pixel_coords = cbind(rownames(coord(msidata)), coord(msidata))
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117 colnames(pixel_coords)[1] = "pixel_coordinates"
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118
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119 ###position_df = cbind(pixel_coords, valid_annotations[,2])
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120 position_df = merge(pixel_coords, valid_annotations)
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121 position_df\$annotation = factor(position_df\$annotation)
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122
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123 }else{
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124 msidata = msidata[,0]
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125 validpixels=0}
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126
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127 ############ Pixels in two columns format: x and y in different columns #############
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128
5
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129 #elif str($pixels_cond.pixel_filtering) == "two_columns":
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130 print("two columns")
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131
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132 ## read tabular file, count number of rows (= number of pixels), extract dataframe with x,y,annotation (for QC), count number of valid pixels
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133 input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE,
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134 stringsAsFactors = FALSE)
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135 startingrow = $pixels_cond.pixel_header+1
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136 numberpixels = length(startingrow:nrow(input_list))
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137 inputpixels = input_list[startingrow:nrow(input_list),c($pixels_cond.pixel_column_x, $pixels_cond.pixel_column_y, $pixels_cond.annotation_column_xy)]
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138 colnames(inputpixels) = c("x", "y", "annotation")
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139 position_df = merge(coord(msidata)[,1:2], inputpixels, by=c("x", "y"), all.x=TRUE)
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140 validpixels = nrow(position_df)
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141 colnames(position_df)[3] = "annotation"
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142 position_df\$annotation = factor(position_df\$annotation)
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143
6
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144 ## for valid pixels: filter file for pixels
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145 if (validpixels != 0){
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146 pixelvector = character()
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147 for (pixel in 1:nrow(position_df)){
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148 pixelvector[pixel] = paste0("x = ", position_df[pixel,1],", ", "y = ", position_df[pixel,2])}
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149 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]
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150 msidata = msidata[,pixelsofinterest]
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151 }else{
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152 validpixels=0}
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153
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154 ########### Pixels wihin x and y minima and maxima are kept ###################
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155
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156 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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157 print("pixel range")
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158
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159 numberpixels = "range"
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160 validpixels = "range"
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161
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162 ## only filter pixels if at least one pixel will be left
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163 if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0 & sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0){
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164
5
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165 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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166 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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167 }else{
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168 msidata = msidata[,0]
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169 print("no valid pixel found")}
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170
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171 ## update position_df for filtered pixels
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172 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))
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173 colnames(position_df)[3] = "annotation"
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174 position_df\$annotation = factor(position_df\$annotation)
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175
5
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176 #elif str($pixels_cond.pixel_filtering) == "none":
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177 print("no pixel filtering")
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178
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179 numberpixels = 0
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180 validpixels = 0
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181
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182 #end if
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183
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184 }else{
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185 print("Inputfile has no intensities > 0")
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186 }
0
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187
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188 ################################# filtering of features ######################
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189 ##############################################################################
0
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190
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191 ####################### Keep m/z from tabular file #########################
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192
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193 ## feature filtering only when pixels/features/intensities are left
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194 npeaks_before_filtering= sum(spectra(msidata)[]>0, na.rm=TRUE)
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195
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196
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197
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198 if (npeaks_before_filtering > 0)
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199
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200 {
0
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201
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202 #if str($features_cond.features_filtering) == "features_list":
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203 print("feature list")
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204
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205 ## read tabular file, define starting row, extract and count valid features
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206 input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE)
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207 startingrow = $features_cond.feature_header+1
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208 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column]
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209 numberfeatures = length(extracted_features)
2
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210
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211 ## find out type of tabular file (numeric or character format)
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212 if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE){
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213
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214 ### if input is in numeric format
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215 if (class(extracted_features) == "numeric"){
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216 ### max digits given in the input file will be used to match m/z but the maximum is 4
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217 max_digits = max(nchar(matrix(unlist(strsplit(as.character(extracted_features), "\\.")), ncol=2, byrow=TRUE)[,2]))
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218 if (max_digits >4)
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219 {
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220 max_digits = 4
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221 }
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222
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223 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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224 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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225 validmz = length(unique(featuresofinterest))
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226 }else{
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227 validmz = 0
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228 featuresofinterest = 0}
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229
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230 ### if input is already in character format (m/z = 800.01)
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231
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232 }else{
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233 validfeatures = extracted_features %in% names(features(msidata))
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234 featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
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235 validmz = sum(validfeatures)}
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236
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237 ### filter msidata for valid features
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238
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239 msidata = msidata[featuresofinterest,]
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240
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241 ############### features within a given range are kept #####################
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242
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243 #elif str($features_cond.features_filtering) == "features_range":
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244 print("feature range")
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245
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246 numberfeatures = "range"
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247 validmz = "range"
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248
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249 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){
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250 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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251 }else{
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252 msidata = msidata[0,]
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253 print("no valid mz range")}
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254
5
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255 ############### Remove m/z from tabular file #########################
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256
5
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257 #elif str($features_cond.features_filtering) == "remove_features":
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258 print("remove features")
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259
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260 ### Tabular file contains mz either as numbers or in the format mz = 800.01
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261
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262 input_features = read.delim("$inputfeatures_removal", header = FALSE, stringsAsFactors = FALSE)
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263 startingrow = $features_cond.removal_header+1
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264 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.removal_column]
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265 numberfeatures = length(extracted_features)
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266
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267 if (grepl("m/z = ", input_features[startingrow,$features_cond.removal_column])==TRUE){
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268
5
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269 ### if input is mz = 800 character format
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270 print("input is in format mz = 400")
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271 validfeatures = extracted_features %in% names(features(msidata))
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272 validmz = sum(validfeatures)
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273 filtered_features = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
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274 featuresofinterest = mz(msidata)[filtered_features]
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275
5
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276 ### if input is numeric:
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277 }else{
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278 if (class(extracted_features) == "numeric"){
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279 print("input is numeric")
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280 featuresofinterest = extracted_features
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281 validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata)))
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282 }else{featuresofinterest = 0
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283 validmz = 0}
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284 }
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285
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286 ### Here starts removal of features:
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287
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288 plusminus = $features_cond.removal_plusminus
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289
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290 mass_to_remove = numeric()
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291 if (sum(featuresofinterest) > 0){
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292 for (masses in featuresofinterest){
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293 #if str($features_cond.units_removal) == "ppm":
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294 plusminus = masses * $features_cond.removal_plusminus/1000000
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295 #end if
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296 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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297 mass_to_remove = append(mass_to_remove, current_mass)}
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298 msidata= msidata[-mass_to_remove, ]
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299 }else{print("No features were removed as they were not fitting to m/z values and/or range")}
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300
1
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301
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302 #elif str($features_cond.features_filtering) == "none":
1
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303
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304 print("no feature filtering")
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305 validmz = 0
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306 numberfeatures = 0
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307
5
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308 #end if
0
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309
5
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310 ## save msidata as Rfile
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311 save(msidata, file="$msidata_filtered")
0
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312
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313 }else{
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314 print("Inputfile or file filtered for pixels has no intensities > 0")
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315 numberfeatures = NA
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316 validmz = NA
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317 }
0
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318
6
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319 #################### QC numbers #######################
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320
0
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321
5
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322 ## Number of features (m/z)
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323 maxfeatures2 = length(features(msidata))
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324 ## Range m/z
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325 minmz2 = round(min(mz(msidata)), digits=2)
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326 maxmz2 = round(max(mz(msidata)), digits=2)
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327 ## Number of spectra (pixels)
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328 pixelcount2 = length(pixels(msidata))
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329 ## Range x coordinates
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330 minimumx2 = min(coord(msidata)[,1])
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331 maximumx2 = max(coord(msidata)[,1])
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332 ## Range y coordinates
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333 minimumy2 = min(coord(msidata)[,2])
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334 maximumy2 = max(coord(msidata)[,2])
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335 ## Number of intensities > 0
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336 npeaks2= sum(spectra(msidata)[]>0, na.rm=TRUE)
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337 ## Spectra multiplied with m/z (potential number of peaks)
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338 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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339 ## Percentage of intensities > 0
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340 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2)
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341 ## Number of empty TICs
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342 TICs2 = colSums(spectra(msidata)[], na.rm=TRUE)
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343 NumemptyTIC2 = sum(TICs2 == 0)
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344 ## median TIC
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345 medint2 = round(median(TICs2), digits=2)
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346
5
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347 properties = c("Number of m/z features",
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348 "Range of m/z values",
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349 "Number of pixels",
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350 "Range of x coordinates",
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351 "Range of y coordinates",
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352 "Intensities > 0",
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353 "Median TIC per pixel",
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354 "Number of zero TICs",
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355 "pixel overview",
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356 "feature overview")
0
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357
5
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358 before = c(paste0(maxfeatures),
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359 paste0(minmz, " - ", maxmz),
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360 paste0(pixelcount),
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361 paste0(minimumx, " - ", maximumx),
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362 paste0(minimumy, " - ", maximumy),
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363 paste0(percpeaks, " %"),
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364 paste0(medint),
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365 paste0(NumemptyTIC),
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366 paste0("input pixels: ", numberpixels),
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367 paste0("input mz: ", numberfeatures))
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368
5
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369 filtered = c(paste0(maxfeatures2),
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370 paste0(minmz2, " - ", maxmz2),
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371 paste0(pixelcount2),
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372 paste0(minimumx2, " - ", maximumx2),
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373 paste0(minimumy2, " - ", maximumy2),
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374 paste0(percpeaks2, " %"),
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diff changeset
375 paste0(medint2),
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diff changeset
376 paste0(NumemptyTIC2),
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diff changeset
377 paste0("valid pixels: ", validpixels),
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378 paste0("valid mz: ", validmz))
0
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379
5
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380 property_df = data.frame(properties, before, filtered)
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381
6
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382 ############################### PDF QC ################################
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383
0
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384
5
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385 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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386 plot(0,type='n',axes=FALSE,ann=FALSE)
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387 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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388 grid.table(property_df, rows= NULL)
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389
6
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390 ## QC report with more than value-table: only when pixels/features/intensities are left
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391 if (npeaks2 > 0)
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392 {
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393 ### visual pixel control
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394
7
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395 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
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396 geom_tile(height = 1, width=1)+
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397 coord_fixed()+
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398 ggtitle("Spatial orientation of filtered pixels")+
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399 theme_bw()+
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400 theme(plot.title = element_text(hjust = 0.5))+
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401 theme(text=element_text(family="ArialMT", face="bold", size=12))+
6
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402 theme(legend.position="bottom",legend.direction="vertical")+
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403 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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diff changeset
404
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diff changeset
405 print(pixel_image)
0
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406
5
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407 ### control features which are removed
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408 hist(mz(msidata), xlab="m/z", main="Kept m/z values")
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409 #if str($features_cond.features_filtering) == "none":
6
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410 print("no difference histogram as no m/z filtering took place")
5
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411 #else:
1
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412
5
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413 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){
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414 print("No difference in m/z values before and after filtering, no histogram drawn")
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415 }else{
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416 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")}
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417 #end if
0
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418
5
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diff changeset
419 dev.off()
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420
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421 ############################### optional intensity matrix ######################
0
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422
5
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423 #if $output_matrix:
0
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424
5
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425 spectramatrix = spectra(msidata)[]
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426 spectramatrix = cbind(mz(msidata),spectramatrix)
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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427 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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428 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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429
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
430 #end if
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431
0
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432 }else{
6
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433 print("Inputfile or filtered file has no intensities > 0")
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434 dev.off()
5
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435 }
0
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436 ]]></configfile>
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437 </configfiles>
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438 <inputs>
3
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439 <param name="infile" type="data" format="imzml,rdata,analyze75"
0
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440 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
1
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441 help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
5
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442 <conditional name="processed_cond">
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443 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
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444 <option value="no_processed" selected="True">not a processed imzML</option>
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445 <option value="processed">processed imzML</option>
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
446 </param>
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447 <when value="no_processed"/>
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448 <when value="processed">
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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449 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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450 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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451 <option value="mz" >mz</option>
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452 <option value="ppm" selected="True" >ppm</option>
3d5ac78fb2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
453 </param>
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diff changeset
454 </when>
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455 </conditional>
6
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456
1
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457 <conditional name="pixels_cond">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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458 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
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459 <option value="none" selected="True">none</option>
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460 <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
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461 <option value="two_columns">tabular file with separate columns for x and y values</option>
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462 <option value="pixel_range">ranges for x and y</option>
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diff changeset
463 </param>
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diff changeset
464 <when value="none"/>
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465 <when value="single_column">
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466 <param name="single_pixels" type="data" format="tabular" label="Pixels in single column for filtering of MSI data"
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467 help="tabular file with pixels of interest in the form x = 1, y = 1"/>
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468 <param name="pixel_column" data_ref="single_pixels" label="Column with pixels" type="data_column"/>
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469 <param name="annotation_column" data_ref="single_pixels" label="Column with annotations for each pixel" type="data_column"/>
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470 <param name="pixel_header" label="Number of header lines to skip" value="0" type="integer"/>
1
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471 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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472 <when value="two_columns">
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473 <param name="two_columns_pixel" type="data" format="tabular" label="Pixels in two columns for filtering of MSI data"
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474 help="tabular file with pixels of interest in two separate columns"/>
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475 <param name="pixel_column_x" data_ref="two_columns_pixel" label="Column with x values" type="data_column"/>
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476 <param name="pixel_column_y" data_ref="two_columns_pixel" label="Column with y values" type="data_column"/>
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477 <param name="annotation_column_xy" data_ref="two_columns_pixel" label="Column with annotations" type="data_column"/>
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478 <param name="pixel_header" label="Number of header lines to skip" value="0" type="integer"/>
1
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479 </when>
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480 <when value="pixel_range">
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481 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
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482 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
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483 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
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484 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
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485 </when>
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486 </conditional>
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487
1
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488 <conditional name="features_cond">
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489 <param name="features_filtering" type="select" label="Select feature filtering option">
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490 <option value="none" selected="True">none</option>
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491 <option value="features_list">keep features (tabular input)</option>
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492 <option value="features_range">keep features within a range (manual input)</option>
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493 <option value="remove_features">remove features (tabular input)</option>
1
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494 </param>
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495 <when value="none"/>
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496 <when value="features_list">
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497 <param name="inputfeatures" type="data" format="tabular" label="Features for filtering of MSI data" help="tabular file with m/z of interest either as numbers (800.05) or in the form m/z = 800.05"/>
1
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498 <param name="feature_column" data_ref="inputfeatures" label="Column with features" type="data_column"/>
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499 <param name="feature_header" label="Number of header lines to skip" value="0" type="integer"/>
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500 </when>
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501 <when value="features_range">
3
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502 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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503 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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504 </when>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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505 <when value="remove_features">
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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506 <param name="inputfeatures_removal" type="data" format="tabular" label="Features for filtering of MSI data" help="tabular file with m/z to be removed either as numbers (800.05) or in the form m/z = 800.05"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
507 <param name="removal_column" data_ref="inputfeatures_removal" label="Column with features" type="data_column"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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508 <param name="removal_header" label="Number of header lines to skip" value="0" type="integer"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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509 <param name="removal_plusminus" type="float" value="20" label="Window in which m/z will be removed" help="This value will be added and substracted from the given input value"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
510 <param name="units_removal" type="select" display = "radio" optional = "False" label="units">
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
511 <option value="ppm" selected="True">ppm</option>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
512 <option value="Da">Da</option>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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513 </param>
6
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514 </when>
1
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parents: 0
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515 </conditional>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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516 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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517 </inputs>
6
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518
0
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519 <outputs>
3
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520 <data format="rdata" name="msidata_filtered" label="$infile.display_name filtered"/>
6
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521 <data format="pdf" name="filtering_qc" from_work_dir="filtertool_QC.pdf" label = "$infile.display_name filtered_QC"/>
3
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522 <data format="tabular" name="matrixasoutput" label="$infile.display_name filtered_matrix">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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523 <filter>output_matrix</filter>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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524 </data>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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525 </outputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
526 <tests>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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527 <test expect_num_outputs="2">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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528 <param name="infile" value="" ftype="imzml">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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529 <composite_data value="Example_Continuous.imzML"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
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530 <composite_data value="Example_Continuous.ibd"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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531 </param>
1
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galaxyp
parents: 0
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532 <param name="pixel_filtering" value="single_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
533 <param name="single_pixels" ftype="tabular" value = "inputpixels.tabular"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
534 <param name="pixel_column" value="1"/>
7
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parents: 6
diff changeset
535 <param name="annotation_column" value="2"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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536 <param name="features_filtering" value="features_list"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
537 <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
538 <param name="feature_column" value="2"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
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539 <param name="feature_header" value="1"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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540 <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/>
7
73b5a754f35c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 620a469e20836b921b6c0147421c8a4268b66ebd
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parents: 6
diff changeset
541 <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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542 </test>
1
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parents: 0
diff changeset
543 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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544 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
545 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
546 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
547 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
548 <param name="pixel_filtering" value="pixel_range"/>
2
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parents: 1
diff changeset
549 <param name="min_x_range" value="10"/>
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parents: 1
diff changeset
550 <param name="max_x_range" value="20"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
551 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
552 <param name="max_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
553 <output name="filtering_qc" file="imzml_filtered2.pdf" compare="sim_size" delta="20000"/>
7
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diff changeset
554 <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
555 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
556 <test expect_num_outputs="3">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
557 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
558 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
559 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
560 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
561 <param name="pixel_filtering" value="pixel_range"/>
2
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parents: 1
diff changeset
562 <param name="min_x_range" value="1"/>
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parents: 1
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563 <param name="max_x_range" value="20"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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564 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
565 <param name="max_y_range" value="2"/>
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diff changeset
566 <param name="features_filtering" value="features_range"/>
3
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567 <param name="min_mz" value="350" />
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
568 <param name="max_mz" value="500"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
569 <param name="output_matrix" value="True"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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570 <output name="filtering_qc" file="imzml_filtered3.pdf" compare="sim_size" delta="20000"/>
7
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diff changeset
571 <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size"/>
1
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galaxyp
parents: 0
diff changeset
572 <output name="matrixasoutput" file="imzml_matrix3.tabular"/>
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diff changeset
573 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
574 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
575 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
576 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
577 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
578 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
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579 <param name="pixel_filtering" value="two_columns"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
580 <param name="two_columns_pixel" ftype="tabular" value = "inputpixels_2column.tabular"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
581 <param name="pixel_column_x" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
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582 <param name="pixel_column_y" value="3"/>
6
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parents: 5
diff changeset
583 <param name="annotation_column_xy" value="2"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
584 <output name="filtering_qc" file="imzml_filtered4.pdf" compare="sim_size" delta="20000"/>
7
73b5a754f35c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 620a469e20836b921b6c0147421c8a4268b66ebd
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parents: 6
diff changeset
585 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
586 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
587 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
588 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
589 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
590 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
591 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
592 <param name="pixel_filtering" value="pixel_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
593 <param name="min_x_range" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
594 <param name="max_x_range" value="10"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
595 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
596 <param name="max_y_range" value="20"/>
3
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parents: 2
diff changeset
597 <param name="features_filtering" value="features_list"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 2
diff changeset
598 <param name="inputfeatures" ftype="tabular" value = "featuresofinterest5.tabular"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 2
diff changeset
599 <param name="feature_column" value="1"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
600 <param name="feature_header" value="0"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
601 <output name="filtering_qc" file="imzml_filtered5.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
602 <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
603 </test>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
604 <test expect_num_outputs="3">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
605 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
606 <composite_data value="Analyze75.hdr"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
607 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
608 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
609 </param>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
610 <param name="pixel_filtering" value="single_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
611 <param name="single_pixels" ftype="tabular" value = "inputpixels2.tabular"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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parents:
diff changeset
612 <param name="pixel_column" value="1"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
613 <param name="features_filtering" value="features_list"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
614 <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
615 <param name="feature_column" value="1"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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616 <param name="output_matrix" value="True"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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617 <output name="filtering_qc" file="analyze_filtered.pdf" compare="sim_size" delta="20000"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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618 <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" />
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
619 <output name="matrixasoutput" file="analyze_matrix.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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620 </test>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
621 <test expect_num_outputs="2">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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622 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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623 <composite_data value="Analyze75.hdr"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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624 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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625 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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626 </param>
1
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627 <output name="filtering_qc" file="analyze75_filtered2.pdf" compare="sim_size" delta="20000"/>
2
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parents: 1
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628 <output name="msidata_filtered" file="analyze_filteredoutside.RData" compare="sim_size" />
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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629 </test>
6
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630 <test expect_num_outputs="3">
2
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diff changeset
631 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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632 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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633 <param name="outputs_select" value="no_quality_control"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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634 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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635 <param name="output_matrix" value="True"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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636 <output name="matrixasoutput" file="rdata_matrix.tabular"/>
1
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637 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size" />
6
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diff changeset
638 <output name="filtering_qc" file="rdata_notfiltered.pdf" compare="sim_size" />
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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639 </test>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
640 </tests>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
641 <help>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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642 <![CDATA[
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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643
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
644 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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645
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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646 This tool provides provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
647
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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648 Input data: 3 types of input data can be used:
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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649
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
650 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
651 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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652 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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653
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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654
2
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diff changeset
655 Options:
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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656
6
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diff changeset
657 - pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible)
3
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658 - m/z feature filtering: can use a tabular file containing m/z of interest or by defining a range for the m/z values (! numeric input will be rounded to 2 digits before matching to m/z!)
6
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659 - m/z feature removing: perturbing m/z such as matrix contaminants can be removed by specifying their m/z in a tabular file and optionally set a window (window in ppm or m/z in which peaks should be removed)
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d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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660
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22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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661
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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662 Output:
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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663
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d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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664 - imzML file filtered for pixels and/or m/z
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bf61fc662615 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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665 - optional: pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z
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d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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666 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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667
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22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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668
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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669 Tip:
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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670
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d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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671 - It is recommended to use the filtering tool only for m/z which have been extracted from the same dataset. If you have m/z from dataset A and you want to use them to filter dataset B, first find the corresponding (closest) features in dataset B by using the tool "Join two files on column allowing a small difference". Afterwards use the corresponding feature m/z from dataset A to filter dataset B.
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22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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672
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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673
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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674 ]]>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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675 </help>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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676 <citations>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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677 <citation type="doi">10.1093/bioinformatics/btv146</citation>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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678 </citations>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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679 </tool>