Mercurial > repos > galaxyp > msi_filtering

annotate msi_filtering.xml @ 3:d51c3c814d57 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
author galaxyp
date Mon, 11 Jun 2018 17:33:40 -0400
parents 22db5eb94e50
children bf61fc662615
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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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1 <tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.1">
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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 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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10 #if $infile.ext == 'imzml'
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11 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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12 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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13 #elif $infile.ext == 'analyze75'
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14 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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15 ln -s '${infile.extra_files_path}/img' infile.img &&
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16 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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17 #else
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18 ln -s $infile infile.RData &&
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19 #end if
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20 cat '${MSI_subsetting}' &&
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21 echo ${MSI_subsetting} &&
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22 Rscript '${MSI_subsetting}'
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24 ]]>
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25 </command>
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26 <configfiles>
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27 <configfile name="MSI_subsetting"><![CDATA[
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29
2
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30 ################################# load libraries and read file #################
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33 library(Cardinal)
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34 library(gridExtra)
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36 #if $infile.ext == 'imzml'
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37 msidata = readImzML('infile')
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38 #elif $infile.ext == 'analyze75'
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39 msidata = readAnalyze('infile')
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40 #else
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41 load('infile.RData')
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42 #end if
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43
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44 ########################### optional QC numbers ########################
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45
1
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46 #if $outputs.outputs_select == "quality_control":
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47
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48 ## Number of features (m/z)
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49 maxfeatures = length(features(msidata))
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50 ## Range m/z
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51 minmz = round(min(mz(msidata)), digits=2)
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52 maxmz = round(max(mz(msidata)), digits=2)
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53 ## Number of spectra (pixels)
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54 pixelcount = length(pixels(msidata))
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55 ## Range x coordinates
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56 minimumx = min(coord(msidata)[,1])
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57 maximumx = max(coord(msidata)[,1])
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58 ## Range y coordinates
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59 minimumy = min(coord(msidata)[,2])
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60 maximumy = max(coord(msidata)[,2])
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61 ## Number of intensities > 0
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62 npeaks= sum(spectra(msidata)[]>0)
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63 ## Spectra multiplied with m/z (potential number of peaks)
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64 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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65 ## Percentage of intensities > 0
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66 percpeaks = round(npeaks/numpeaks*100, digits=2)
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67 ## Number of empty TICs
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68 TICs = colSums(spectra(msidata)[])
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69 NumemptyTIC = sum(TICs == 0)
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70 ## median TIC
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71 medint = round(median(TICs), digits=2)
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72 ## Store features for QC plot
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73 featuresinfile = mz(msidata)
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74
0
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75 #end if
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76
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77 ###################################### Filtering of pixels #####################
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78 ################################################################################
0
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79
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80 #################### Pixels in the one column format "x=,y=" #####################
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82 #if str($pixels_cond.pixel_filtering) == "single_column":
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83 print("single column")
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84
3
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85 input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE)
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86 numberpixels = length(input_list[,$pixels_cond.pixel_column])
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87 valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata))
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88 validpixels = sum(valid_entries)
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89
3
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90 if (validpixels != 0){
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91 pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]
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92 msidata = msidata[,pixelsofinterest]
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93 }else{
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94 msidata = msidata[,0]
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95 validpixels=0}
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96
3
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97 ############ Pixels in two columns format: x and y in different columns #############
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98
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99 #elif str($pixels_cond.pixel_filtering) == "two_columns":
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100 print("two columns")
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101
3
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102 input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE,
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103 stringsAsFactors = FALSE)
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104 numberpixels = length(input_list[,$pixels_cond.pixel_column_x])
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105
3
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106 inputpixel_x = input_list[,$pixels_cond.pixel_column_x]
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107 inputpixel_y = input_list[,$pixels_cond.pixel_column_y]
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108 inputpixels = cbind(inputpixel_x, inputpixel_y)
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109 colnames(inputpixels) = c("x", "y")
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110 valid_rows = merge(inputpixels, coord(msidata)[,1:2])
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111 validpixels = nrow(valid_rows)
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112
3
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113 if (validpixels != 0){
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114 pixelvector = character()
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115 for (pixel in 1:nrow(valid_rows)){
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116 pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])}
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117 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]
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118 msidata = msidata[,pixelsofinterest]
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119 }else{
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120 validpixels=0}
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121
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122 ########### Pixels wihin x and y minima and maxima are kept ###################
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123
1
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124 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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125 print("pixel range")
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126
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127 numberpixels = "range"
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128 validpixels = "range"
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129
2
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130 ## only filter pixels if at least one pixel will be left
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131
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132 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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133 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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134 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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135 }else{
2
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136 msidata = msidata[,0]
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137 print("no valid pixel found")}
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138
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139 #elif str($pixels_cond.pixel_filtering) == "none":
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140 print("no pixel filtering")
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141
0
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142 numberpixels = 0
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143 validpixels = 0
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144
0
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145 #end if
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146
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147
3
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148 ###################################### filtering of features ######################
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149 ##################################################################################
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150
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151 ######################## Keep m/z from tabular file #########################
2
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152
1
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153 #if str($features_cond.features_filtering) == "features_list":
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154 print("feature list")
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155
1
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156 input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE)
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157 startingrow = $features_cond.feature_header+1
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158 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column]
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159 numberfeatures = length(extracted_features)
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160
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161 if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE){
1
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162
2
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163 ### if input is in numeric format
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164 if (class(extracted_features) == "numeric"){
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165 ### max digits given in the input file will be used to match m/z
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166 max_digits = max(nchar(matrix(unlist(strsplit(as.character(extracted_features), "\\.")), ncol=2, byrow=TRUE)[,2]))
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167 validfeatures = extracted_features %in% round(mz(msidata),max_digits)
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168 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% extracted_features[validfeatures]]
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169 validmz = length(unique(featuresofinterest))
1
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170 }else{
3
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171 validmz = 0
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172 featuresofinterest = 0}
2
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173
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174 ### if input is already in character format (m/z = 800.01)
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175
3
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176 }else{
1
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177 validfeatures = extracted_features %in% names(features(msidata))
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178 featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
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179 validmz = sum(validfeatures)}
1
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180
2
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181 ### filter msidata for valid features
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182
1
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183 msidata = msidata[featuresofinterest,]
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184
3
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185 ############### features within a given range are kept #########################
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186
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187 #elif str($features_cond.features_filtering) == "features_range":
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188 print("feature range")
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189
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190 numberfeatures = "range"
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191 validmz = "range"
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192
3
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193 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){
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194 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
2
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195 }else{
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196 msidata = msidata[0,]
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197 print("no valid mz range")}
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198
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199 ############### Remove m/z from tabular file #########################
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200
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201 #elif str($features_cond.features_filtering) == "remove_features":
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202 print("remove features")
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203
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204 ### Tabular file contains mz either as numbers or in the format mz = 800.01
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205
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206 input_features = read.delim("$inputfeatures_removal", header = FALSE, stringsAsFactors = FALSE)
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207 startingrow = $features_cond.removal_header+1
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208 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.removal_column]
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209 numberfeatures = length(extracted_features)
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210
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211 if (grepl("m/z = ", input_features[startingrow,$features_cond.removal_column])==TRUE){
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212
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213 ### if input is mz = 800 character format
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214 print("input is in format mz = 400")
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215 validfeatures = extracted_features %in% names(features(msidata))
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216 validmz = sum(validfeatures)
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217 filtered_features = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
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218 featuresofinterest = mz(msidata)[filtered_features]
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219
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220 ### if input is numeric:
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221 }else{
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222 if (class(extracted_features) == "numeric"){
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223 print("input is numeric")
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224 featuresofinterest = extracted_features
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225 validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata)))
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226 }else{featuresofinterest = 0
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227 validmz = 0}
1
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228 }
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229
3
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230 ### Here starts removal of features:
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231
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232 plusminus = $features_cond.removal_plusminus
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233
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234 mass_to_remove = numeric()
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235 if (sum(featuresofinterest) > 0){
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236 for (masses in featuresofinterest){
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237 #if str($features_cond.units_removal) == "ppm":
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238 plusminus = masses * $features_cond.removal_plusminus/1000000
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239 #end if
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240 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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241 mass_to_remove = append(mass_to_remove, current_mass)}
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242 msidata= msidata[-mass_to_remove, ]
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243 }else{print("No features were removed as they were not fitting to m/z values and/or range")}
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244
1
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245
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246 #elif str($features_cond.features_filtering) == "none":
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247
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248 print("no feature filtering")
2
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249 validmz = 0
0
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250 numberfeatures = 0
3
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251
0
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252 #end if
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253
3
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254 ## save msidata as Rfile
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255 save(msidata, file="$msidata_filtered")
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256
3
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257 #################### optional QC numbers #######################
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258
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259 #if $outputs.outputs_select == "quality_control":
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260
3
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261 ## Number of features (m/z)
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262 maxfeatures2 = length(features(msidata))
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263 ## Range m/z
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264 minmz2 = round(min(mz(msidata)), digits=2)
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265 maxmz2 = round(max(mz(msidata)), digits=2)
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266 ## Number of spectra (pixels)
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267 pixelcount2 = length(pixels(msidata))
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268 ## Range x coordinates
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269 minimumx2 = min(coord(msidata)[,1])
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270 maximumx2 = max(coord(msidata)[,1])
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271 ## Range y coordinates
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272 minimumy2 = min(coord(msidata)[,2])
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273 maximumy2 = max(coord(msidata)[,2])
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274 ## Number of intensities > 0
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275 npeaks2= sum(spectra(msidata)[]>0)
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276 ## Spectra multiplied with m/z (potential number of peaks)
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277 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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278 ## Percentage of intensities > 0
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279 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2)
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280 ## Number of empty TICs
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281 TICs2 = colSums(spectra(msidata)[])
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282 NumemptyTIC2 = sum(TICs2 == 0)
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283 ## median TIC
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284 medint2 = round(median(TICs2), digits=2)
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285
3
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286 properties = c("Number of m/z features",
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287 "Range of m/z values [Da]",
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288 "Number of pixels",
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289 "Range of x coordinates",
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290 "Range of y coordinates",
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291 "Intensities > 0",
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292 "Median TIC per pixel",
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293 "Number of zero TICs",
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294 "pixel overview",
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295 "feature overview")
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296
3
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297 before = c(paste0(maxfeatures),
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298 paste0(minmz, " - ", maxmz),
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299 paste0(pixelcount),
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300 paste0(minimumx, " - ", maximumx),
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301 paste0(minimumy, " - ", maximumy),
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302 paste0(percpeaks, " %"),
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303 paste0(medint),
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304 paste0(NumemptyTIC),
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305 paste0("input pixels: ", numberpixels),
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306 paste0("input mz: ", numberfeatures))
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307
3
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308 filtered = c(paste0(maxfeatures2),
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309 paste0(minmz2, " - ", maxmz2),
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310 paste0(pixelcount2),
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311 paste0(minimumx2, " - ", maximumx2),
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312 paste0(minimumy2, " - ", maximumy2),
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313 paste0(percpeaks2, " %"),
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314 paste0(medint2),
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315 paste0(NumemptyTIC2),
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316 paste0("valid pixels: ", validpixels),
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317 paste0("valid mz: ", validmz))
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318
3
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319 property_df = data.frame(properties, before, filtered)
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320
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321 ############################### optional PDF QC ################################
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322
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323 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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324 plot(0,type='n',axes=FALSE,ann=FALSE)
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325 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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326 grid.table(property_df, rows= NULL)
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327
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328 ### heatmap image as visual pixel control
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329 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
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330 image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none",
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331 main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2))
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332
3
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333 ### control features which are left
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334 plot(featuresinfile, rep(1,length(featuresinfile)), yaxt="n", ylab=NA, xlab="m/z values", col="red", ylim=c(0.8, 1.1), main="Distribution of m/z values")
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335 lines(mz(msidata),rep(0.9, length(mz(msidata))), col="green", type="p")
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336 legend("top", horiz=TRUE, legend = c("before", "filtered"), fill = c("red", "green"))
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337 }else{
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338 print("file has no features or pixels left")}
1
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339
0
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340 dev.off()
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341
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342 #end if
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343
3
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344 ############################### optional intensity matrix ######################
0
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345
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346 #if $output_matrix:
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347
3
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348 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
0
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349 spectramatrix = spectra(msidata)
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350 rownames(spectramatrix) = mz(msidata)
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351 newmatrix = rbind(pixels(msidata), spectramatrix)
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352 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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353 }else{
3
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354 print("file has no features or pixels left")}
0
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355
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356 #end if
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357
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358
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359 ]]></configfile>
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360 </configfiles>
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361 <inputs>
3
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362 <param name="infile" type="data" format="imzml,rdata,analyze75"
0
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363 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
1
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364 help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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365 <conditional name="pixels_cond">
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366 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
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367 <option value="none" selected="True">none</option>
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368 <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
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369 <option value="two_columns">tabular file with separate columns for x and y values</option>
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370 <option value="pixel_range">ranges for x and y</option>
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371 </param>
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372 <when value="none"/>
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373 <when value="single_column">
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374 <param name="single_pixels" type="data" format="tabular" label="Pixels in single column for filtering of MSI data"
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375 help="tabular file with pixels of interest in the form x = 1, y = 1"/>
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376 <param name="pixel_column" data_ref="single_pixels" label="Column with pixels" type="data_column"/>
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377 </when>
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378 <when value="two_columns">
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379 <param name="two_columns_pixel" type="data" format="tabular" label="Pixels in two columns for filtering of MSI data"
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380 help="tabular file with pixels of interest in two separate columns"/>
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381 <param name="pixel_column_x" data_ref="two_columns_pixel" label="Column with x values" type="data_column"/>
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382 <param name="pixel_column_y" data_ref="two_columns_pixel" label="Column with y values" type="data_column"/>
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383 </when>
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384 <when value="pixel_range">
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385 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
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386 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
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387 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
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388 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
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389 </when>
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390 </conditional>
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391 <conditional name="features_cond">
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392 <param name="features_filtering" type="select" label="Select feature filtering option">
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393 <option value="none" selected="True">none</option>
3
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394 <option value="features_list">keep features (tabular input)</option>
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395 <option value="features_range">keep features within a range (manual input)</option>
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396 <option value="remove_features">remove features (tabular input)</option>
1
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397 </param>
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398 <when value="none"/>
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399 <when value="features_list">
3
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400 <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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401 <param name="feature_column" data_ref="inputfeatures" label="Column with features" type="data_column"/>
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402 <param name="feature_header" label="Number of header lines to skip" value="0" type="integer"/>
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403 </when>
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404 <when value="features_range">
3
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405 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
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406 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/>
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407 </when>
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408 <when value="remove_features">
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409 <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
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410 <param name="removal_column" data_ref="inputfeatures_removal" label="Column with features" type="data_column"/>
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411 <param name="removal_header" label="Number of header lines to skip" value="0" type="integer"/>
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412 <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"/>
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413 <param name="units_removal" type="select" display = "radio" optional = "False" label="units">
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414 <option value="ppm" selected="True">ppm</option>
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415 <option value="Da">Da</option>
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416 </param>
1
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417 </when>
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418 </conditional>
0
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419 <conditional name="outputs">
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420 <param name="outputs_select" type="select" label="Quality control output">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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421 <option value="quality_control" selected="True">yes</option>
1
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422 <option value="no_quality_control">no</option>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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423 </param>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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424 <when value="quality_control">
3
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425 <param name="inputmz" type="float" value="1296.7" label="M/z for which a heatmap image will be drawn" help="Use a m/z which is still present in all pixels to control if the pixel filtering went well"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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426 <param name="plusminus_dalton" value="0.25" type="float" label="Range for m/z value" help="plusminus m/z window"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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427 </when>
1
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428 <when value="no_quality_control"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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429 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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430 <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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431 </inputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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432 <outputs>
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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433 <data format="rdata" name="msidata_filtered" label="$infile.display_name filtered"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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434 <data format="pdf" name="filtering_qc" from_work_dir="filtertool_QC.pdf" label = "$infile.display_name filtered_QC">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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435 <filter>outputs["outputs_select"] == "quality_control"</filter>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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436 </data>
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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437 <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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438 <filter>output_matrix</filter>
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439 </data>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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440 </outputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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441 <tests>
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442 <test expect_num_outputs="2">
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443 <param name="infile" value="" ftype="imzml">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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444 <composite_data value="Example_Continuous.imzML"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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445 <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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446 </param>
1
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447 <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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448 <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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449 <param name="pixel_column" value="1"/>
1
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450 <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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451 <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
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452 <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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453 <param name="feature_header" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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454 <param name="outputs_select" value="quality_control"/>
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455 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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456 <param name="plusminus_dalton" value="0.25"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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457 <output name="filtering_qc" file="imzml_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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458 <output name="msidata_filtered" file="imzml_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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459 </test>
1
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460 <test expect_num_outputs="2">
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461 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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462 <composite_data value="Example_Continuous.imzML"/>
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
463 <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
464 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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465 <param name="pixel_filtering" value="pixel_range"/>
2
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466 <param name="min_x_range" value="10"/>
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467 <param name="max_x_range" value="20"/>
1
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468 <param name="min_y_range" value="2"/>
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diff changeset
469 <param name="max_y_range" value="2"/>
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470 <param name="outputs_select" value="quality_control"/>
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471 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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472 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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473 <output name="filtering_qc" file="imzml_filtered2.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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474 <output name="msidata_filtered" file="imzml_filtered2.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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475 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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476 <test expect_num_outputs="3">
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477 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
478 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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479 <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
480 </param>
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diff changeset
481 <param name="pixel_filtering" value="pixel_range"/>
2
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parents: 1
diff changeset
482 <param name="min_x_range" value="1"/>
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483 <param name="max_x_range" value="20"/>
1
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diff changeset
484 <param name="min_y_range" value="2"/>
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diff changeset
485 <param name="max_y_range" value="2"/>
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486 <param name="features_filtering" value="features_range"/>
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
487 <param name="min_mz" value="350" />
1
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diff changeset
488 <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
489 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
490 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
491 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
492 <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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493 <output name="filtering_qc" file="imzml_filtered3.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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diff changeset
494 <output name="msidata_filtered" file="imzml_filtered3.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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diff changeset
495 <output name="matrixasoutput" file="imzml_matrix3.tabular"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
496 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
497 <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
498 <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
499 <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
500 <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
501 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
502 <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
503 <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
504 <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
diff changeset
505 <param name="pixel_column_y" value="3"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
506 <param name="features_filtering" value="features_list"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
507 <param name="inputfeatures" ftype="tabular" value = "inputcalibrantfile2.txt"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
508 <param name="feature_column" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
509 <param name="feature_header" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
510 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
511 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
512 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
513 <output name="filtering_qc" file="imzml_filtered4.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
514 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
515 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
516 <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
517 <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
518 <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
519 <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
520 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
521 <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
522 <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
galaxyp
parents: 0
diff changeset
523 <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
524 <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
525 <param name="max_y_range" value="20"/>
3
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
526 <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
galaxyp
parents: 2
diff changeset
527 <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
galaxyp
parents: 2
diff changeset
528 <param name="feature_column" value="1"/>
d51c3c814d57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
529 <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
galaxyp
parents: 0
diff changeset
530 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
531 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
532 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
533 <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
galaxyp
parents: 0
diff changeset
534 <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
galaxyp
parents: 0
diff changeset
535 </test>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
536 <test expect_num_outputs="3">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
537 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
538 <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
539 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
540 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
541 </param>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
542 <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
543 <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
galaxyp
parents:
diff changeset
544 <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
galaxyp
parents: 0
diff changeset
545 <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
parents:
diff changeset
546 <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
galaxyp
parents:
diff changeset
547 <param name="feature_column" value="1"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
548 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
549 <param name="outputs_select" value="quality_control"/>
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
550 <param name="inputmz" value="1200"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
551 <param name="plusminus_dalton" value="0.25"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
552 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
553 <param name="output_matrix" value="True"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
554 <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
galaxyp
parents:
diff changeset
555 <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
galaxyp
parents:
diff changeset
556 <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
galaxyp
parents:
diff changeset
557 </test>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
558 <test expect_num_outputs="2">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
559 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
560 <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
561 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
562 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
563 </param>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
564 <conditional name="outputs">
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
565 <param name="outputs_select" value="quality_control"/>
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
566 <param name="inputmz" value="1200"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
567 <param name="plusminus_dalton" value="0.25"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
568 </conditional>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
569 <output name="filtering_qc" file="analyze75_filtered2.pdf" compare="sim_size" delta="20000"/>
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
570 <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
galaxyp
parents:
diff changeset
571 </test>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
572 <test expect_num_outputs="2">
2
22db5eb94e50 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
573 <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
galaxyp
parents:
diff changeset
574 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
575 <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
galaxyp
parents:
diff changeset
576 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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577 <param name="output_matrix" value="True"/>
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578 <output name="matrixasoutput" file="rdata_matrix.tabular"/>
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579 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size" />
0
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580 </test>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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581 </tests>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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582 <help>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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583 <![CDATA[
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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584
2
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585 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
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586
3
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587 This tool provides provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
0
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588
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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589 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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590
2
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591 - 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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592 - 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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593 - 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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594
3
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595
2
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596 Options:
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597
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598 - pixel filtering: can use a tabular file containing x and y coordinates or by defining a range for x and y by hand
3
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599 - 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!)
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600 - m/z feature removing: infering 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 Da in which peaks should be removed)
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601
2
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602
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603 Output:
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604
3
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605 - imzML file filtered for pixels and/or m/z
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606 - optional: pdf with heatmap showing the pixels that are left after filtering and plot of m/z before and after filtering
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607 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
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608
2
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609
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610 Tip:
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611
3
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612 - 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.
2
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613
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614
0
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615 ]]>
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616 </help>
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617 <citations>
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618 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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619 </citations>
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620 </tool>