Mercurial > repos > galaxyp > cardinal_filtering

annotate filtering.xml @ 15:1990986966c1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
author galaxyp
date Tue, 22 Feb 2022 20:49:33 +0000
parents 105056844497
children 890845926d4b
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0">
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2 <description>tool for filtering mass spectrometry imaging data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.3">r-gridextra</requirement>
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8 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
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9 </expand>
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10 <expand macro="print_version"/>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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14 @INPUT_LINKING@
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15 cat '${MSI_subsetting}' &&
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16 Rscript '${MSI_subsetting}' &&
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17 mkdir $outfile_imzml.files_path &&
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18 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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19 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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20 echo "imzML file:" > $outfile_imzml &&
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21 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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22 ]]>
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23 </command>
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26 <configfiles>
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27 <configfile name="MSI_subsetting"><![CDATA[
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30 ################################# load libraries and read file #################
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33 library(Cardinal)
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34 library(ggplot2)
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35 library(gridExtra)
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39 @READING_MSIDATA_FULLY_COMPATIBLE@
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42 ########################### QC numbers ########################
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44 ## Number of features (m/z)
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45 maxfeatures = nrow(msidata)
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46 ## Range m/z
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47 minmz = round(min(mz(msidata)), digits=2)
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48 maxmz = round(max(mz(msidata)), digits=2)
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49 ## Number of spectra (pixels)
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50 pixelcount = ncol(msidata)
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51 ## Range x coordinates
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52 minimumx = min(coord(msidata)\$x)
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53 maximumx = max(coord(msidata)\$x)
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54 ## Range y coordinates
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55 minimumy = min(coord(msidata)\$y)
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56 maximumy = max(coord(msidata)\$y)
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57 ## Store features for QC plot
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58 featuresinfile = mz(msidata)
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59
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60 all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata)))
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61 colnames(all_df) = c("x", "y", "annotation")
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62
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63 ## Next steps will only run if there are more than 0 pixels/features in the file
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65 if (ncol(msidata)>0 & nrow(msidata) >0)
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66 {
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67 ###################################### Filtering of pixels #####################
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68 ################################################################################
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70 ############ Pixels in two columns format: x and y in different columns #############
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72 #if str($pixels_cond.pixel_filtering) == "two_columns":
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73 print("two columns")
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75 ## read tabular file
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76 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header,
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77 stringsAsFactors = FALSE)
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78 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)]
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79 input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_")
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80 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
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81 pixelsofinterest = dataset_pixels %in% input_pixels
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82
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83 tryCatch(
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84 {
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85 msidata = msidata[,pixelsofinterest]
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86 if (ncol(msidata) == 0)
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87 {
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88 stop(call.=FALSE)
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89 }
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90 },
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91 error=function(cond) {
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92 ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
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93 message("Error during pixel filtering")
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94 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool")
2
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95 stop(call.=FALSE)
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96 }
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97 )
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98
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99 ## QC values:
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100 numberpixels = nrow(input_list)
0
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101 validpixels=ncol(msidata)
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102
2
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103 ########### Pixels wihin x and y minima and maxima are kept #################
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104
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105 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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106 print("pixel range")
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107
2
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108 ## QC values:
0
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109 numberpixels = "range"
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110 validpixels = "range"
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111
2
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112 tryCatch(
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113 {
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114 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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115 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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116 if (ncol(msidata) == 0)
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117 {
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118 stop(call.=FALSE)
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119 }
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120 },
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121 error=function(cond) {
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122 ## in case one of the ranges was outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
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123 message("Error during pixel filtering")
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124 message("Check that both x and y ranges were inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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125 stop(call.=FALSE)
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126 }
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127 )
1
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128
2
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129 ######################## no pixel filtering ################################
0
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130
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131 #elif str($pixels_cond.pixel_filtering) == "none":
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132 print("no pixel filtering")
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133
2
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134 ## QC values:
0
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135 numberpixels = 0
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136 validpixels = 0
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137
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138 #end if
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139
2
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140 ############################# QC data #####################################
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141
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142 ## dataframe for QC of pixel distribution
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143
6
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144 remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata)))
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145 colnames(remaining_df) = c("x", "y", "annotation")
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146 position_df = rbind(all_df, remaining_df)
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147 position_df[row.names(unique(position_df[,c("x", "y")])),]
2
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148 position_df\$annotation = factor(position_df\$annotation)
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149 gc()
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150
0
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151 }else{
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152 print("Inputfile has no intensities > 0")
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153 }
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154
2
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155 ################################# filtering of features ######################
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156 ##############################################################################
0
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157
2
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158 ####################### Keep m/z from tabular file #########################
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159
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160 ## feature filtering only when pixels/features/intensities are left
1
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161
2
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162
1
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163 if (ncol(msidata) > 0){
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164 if (nrow(msidata) > 0)
1
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165 {
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166
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167 #if str($features_cond.features_filtering) == "features_list":
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168 print("feature list")
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169
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170 ## read tabular file, define starting row, extract and count valid features
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171 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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172 extracted_features = input_features[,$features_cond.feature_column]
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173 numberfeatures = length(extracted_features)
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174
1
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175 if (class(extracted_features) == "numeric"){
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176 ### max digits given in the input file will be used to match m/z but the maximum is 4
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177 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE)
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178
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179 if (max_digits >4)
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180 {
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181 max_digits = 4
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182 }
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183
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184 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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185 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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186 validmz = length(unique(featuresofinterest))
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187
1
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188 }else{
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189 validmz = 0
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190 featuresofinterest = 0}
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191
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192 ### filter msidata for valid features
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193
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194 tryCatch(
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195 {
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196 msidata = msidata[featuresofinterest,]
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197 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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198 if (nrow(msidata) == 0)
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199 {
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200 stop(call.=FALSE)
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201 }
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202 },
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203 error=function(cond) {
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204 ## in case all provided m/z values were outside the m/z range
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205 ## tool is stopped to avoid continuing with wrong data
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206 message("Error during m/z filtering")
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207 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
2
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208 stop(call.=FALSE)
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209 }
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210 )
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211
1
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212
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213 ############### features within a given range are kept #####################
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214
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215 #elif str($features_cond.features_filtering) == "features_range":
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216 print("feature range")
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217
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218 numberfeatures = "range"
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219 validmz = "range"
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220
2
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221 tryCatch(
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222 {
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223 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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224 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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225 if (nrow(msidata) == 0)
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226 {
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227 stop(call.=FALSE)
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228 }
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229 },
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230 error=function(cond) {
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231 ## in case all m/z features were outside the dataset leading to zero m/z features, tool is stopped to avoid continuing with wrong data
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232 message("Error during m/z filtering")
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233 message("Check that the entered m/z range is inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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234 stop(call.=FALSE)
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235 }
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236 )
1
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237
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238 ############### Remove m/z from tabular file #########################
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239
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240 #elif str($features_cond.features_filtering) == "remove_features":
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241 print("remove features")
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242
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243 ## read tabular file, define starting row, extract and count valid features
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244 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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245 extracted_features = input_features[,$features_cond.feature_column]
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246 numberfeatures = length(extracted_features)
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247 if (class(extracted_features) == "numeric"){
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248 print("input is numeric")
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249 featuresofinterest = extracted_features
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250 }else{featuresofinterest = 0}
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251
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252 ### Here starts removal of features:
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253 plusminus = $features_cond.removal_plusminus
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254
2
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255 tryCatch(
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256 {
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257 mass_to_remove = numeric()
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258 for (masses in featuresofinterest){
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259 #if str($features_cond.units_removal) == "ppm":
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260 plusminus = masses * $features_cond.removal_plusminus/1000000
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261 #end if
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262 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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263 mass_to_remove = append(mass_to_remove, current_mass)}
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264 mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove)
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265
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266 msidata= msidata[mass_to_keep, ]
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267 validmz = maxfeatures - nrow(msidata)
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268
2
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269 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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270 if (nrow(msidata) == 0)
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271 {
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272 stop(call.=FALSE)
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273 }
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274 },
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275 error=function(cond) {
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276 message("Error during removal of m/z features")
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277 stop(call.=FALSE)
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278 }
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279 )
0
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280
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281
2
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282
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283 ######################## No m/z filtering ##############################
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284
1
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285 #elif str($features_cond.features_filtering) == "none":
0
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286
1
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287 print("no feature filtering")
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288 validmz = 0
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289 numberfeatures = 0
0
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290
1
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291 #end if
0
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292
1
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293 }else{
2
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294 print("Inputfile has no m/z features")
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295 numberfeatures = NA
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296 validmz = NA
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297 }
0
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298 }else{
2
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299 print("Inputfile or file filtered for pixels has no pixels")
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300 numberfeatures = NA
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301 validmz = NA
0
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302 }
2
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303 gc()
0
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304
2
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305 #################### QC numbers #######################
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306
2
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307 ## Number of features (m/z)
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308 maxfeatures2 = nrow(msidata)
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309 ## Range m/z
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310 minmz2 = round(min(mz(msidata)), digits=2)
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311 maxmz2 = round(max(mz(msidata)), digits=2)
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312 ## Number of spectra (pixels)
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313 pixelcount2 = ncol(msidata)
2
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314 ## Range x coordinates
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315 minimumx2 = min(coord(msidata)\$x)
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316 maximumx2 = max(coord(msidata)\$x)
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317 ## Range y coordinates
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318 minimumy2 = min(coord(msidata)\$y)
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319 maximumy2 = max(coord(msidata)\$y)
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320
2
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321 properties = c("Number of m/z features",
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322 "Range of m/z values",
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323 "Number of pixels",
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324 "Range of x coordinates",
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325 "Range of y coordinates",
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326 "pixel overview",
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327 "feature overview")
0
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328
2
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329 before = c(paste0(maxfeatures),
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330 paste0(minmz, " - ", maxmz),
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331 paste0(pixelcount),
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332 paste0(minimumx, " - ", maximumx),
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333 paste0(minimumy, " - ", maximumy),
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334 paste0("input pixels: ", numberpixels),
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335 paste0("input mz: ", numberfeatures))
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336
2
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337 filtered = c(paste0(maxfeatures2),
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338 paste0(minmz2, " - ", maxmz2),
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339 paste0(pixelcount2),
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340 paste0(minimumx2, " - ", maximumx2),
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341 paste0(minimumy2, " - ", maximumy2),
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342 paste0("valid pixels: ", validpixels),
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343 paste0("valid mz: ", validmz))
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344
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345 property_df = data.frame(properties, before, filtered)
0
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346
2
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347 ########################### PDF QC and MSI output ###########################
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348
2
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349 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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350 plot(0,type='n',axes=FALSE,ann=FALSE)
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351 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier"))
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352 grid.table(property_df, rows= NULL)
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
353
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
354 ## QC report only when pixels/features are left
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
355 if (ncol(msidata)>0 & nrow(msidata) >0)
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
356 {
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
357
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
358 ### visual pixel control
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
359
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
360 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
361 geom_tile(height = 1, width=1)+
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
362 coord_fixed()+
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
363 ggtitle("Spatial orientation of filtered pixels")+
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
364 theme_bw()+
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
365 theme(plot.title = element_text(hjust = 0.5))+
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
366 theme(legend.position="bottom",legend.direction="vertical")+
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
367 guides(fill=guide_legend(ncol=5,byrow=TRUE))
9
e92efed83208 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
368 print(pixel_image + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
369
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
370
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
371 ### visual mz feature control
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
372
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
373 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
374 colnames(kept_df) = c("mz", "legend")
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
375
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
376 mz_removed = setdiff(featuresinfile, mz(msidata))
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
377 removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed)))
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
378 colnames(removed_df) = c("mz", "legend")
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
379 histogram_df = rbind(removed_df,kept_df)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
380
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
381 histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) +
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
382 geom_histogram()+ theme_bw()+
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
383 theme(plot.title = element_text(hjust = 0.5))+
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
384 theme(legend.position="bottom",legend.direction="vertical")+
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
385 labs(title="Overview of filtered m/z", x="m/z", y = "count") +
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
386 guides(fill=guide_legend(ncol=5,byrow=TRUE))
9
e92efed83208 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
387 print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
e92efed83208 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
388
10
a4475567dd22 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
galaxyp
parents: 9
diff changeset
389 dev.off()
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
391 ## save msidata as imzML file, will only work if there is at least 1 m/z left
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
392
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
393 if (maxfeatures2 > 0){
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
394 ## make sure that coordinates are integers
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
395 coord(msidata)\$y = as.integer(coord(msidata)\$y)
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
396 coord(msidata)\$x = as.integer(coord(msidata)\$x)
10
a4475567dd22 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
galaxyp
parents: 9
diff changeset
397 msidata = as(msidata, "MSContinuousImagingExperiment")
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
398 writeImzML(msidata, "out")}
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
399
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
400
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 }else{
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402 print("Inputfile or filtered file has no intensities > 0")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 dev.off()
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 }
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
405
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 ]]></configfile>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407 </configfiles>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
408 <inputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
409 <expand macro="reading_msidata"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
410 <conditional name="pixels_cond">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
411 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
412 <option value="none" selected="True">none</option>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
413 <option value="two_columns">coordinates from tabular file</option>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414 <option value="pixel_range">ranges for x and y (manually)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416 <when value="none"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 <when value="two_columns">
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
418 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates"
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
419 help="Tabular file with two columns: x values and y values"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
420 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
421 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
422 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
423 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
424 <when value="pixel_range">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 </conditional>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <conditional name="features_cond">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 <param name="features_filtering" type="select" label="Select m/z feature filtering option">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 <option value="none" selected="True">none</option>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
435 <option value="features_list">keep m/z (tabular file)</option>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 <option value="features_range">m/z range (manually)</option>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
437 <option value="remove_features">remove m/z (tabular file)</option>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 <when value="none"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440 <when value="features_list">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to keep"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 <when value="features_range">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
445 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
447 <when value="remove_features">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
448 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to remove"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 <param name="removal_plusminus" type="float" value="20" label="Window in which all m/z will be removed" help="This value is the half window size, it will be added and substracted from the given input value"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 <param name="units_removal" type="select" display="radio" optional ="False" label="units">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 <option value="ppm" selected="True">ppm</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 <option value="Da">Da</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 </conditional>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 </inputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 <outputs>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
459 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 </outputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 <tests>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 <param name="pixel_filtering" value="pixel_range"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 <param name="min_x_range" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 <param name="max_x_range" value="20"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 <param name="min_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <param name="max_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 <param name="features_filtering" value="features_range"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
471 <param name="min_mz" value="350"/>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 <param name="max_mz" value="500"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
474 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size">
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
475 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="6"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
476 <extra_files type="file" file="out3.ibd" name="ibd" compare="sim_size"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
477 </output>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
481 <param name="pixel_filtering" value="two_columns"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
482 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 <param name="column_x" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <param name="column_y" value="3"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
486 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
487 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="6"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
488 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
489 </output>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <param name="pixel_filtering" value="pixel_range"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <param name="min_x_range" value="0"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 <param name="max_x_range" value="10"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 <param name="min_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 <param name="max_y_range" value="20"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 <param name="features_filtering" value="features_list"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 <param name="feature_column" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <param name="feature_header" value="0"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
503 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
504 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="6"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
505 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
506 </output>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 <expand macro="infile_analyze75"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
511 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
512 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="6"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
513 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
514 </output>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" />
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
519 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
520 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="6"/>
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
521 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/>
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
522 </output>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 </test>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
524 <test>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
525 <expand macro="processed_infile_imzml"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
526 <conditional name="processed_cond">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
527 <param name="processed_file" value="processed"/>
9
e92efed83208 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
528 <param name="accuracy" value="200"/>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
529 <param name="units" value="ppm"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
530 </conditional>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
531 <param name="pixel_filtering" value="two_columns"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
532 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
533 <param name="column_x" value="1"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
534 <param name="column_y" value="3"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
535 <param name="features_filtering" value="remove_features"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
536 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
537 <param name="feature_column" value="1"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
538 <param name="feature_header" value="0"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
539 <param name="removal_plusminus" value="100"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
540 <param name="units_removal" value="ppm"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
541 <output name="QC_overview" file="imzml_filtered8.pdf" compare="sim_size"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
542 <output name="outfile_imzml" ftype="imzml" file="out8.imzml.txt" compare="sim_size">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
543 <extra_files type="file" file="out8.imzml" name="imzml" lines_diff="6"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
544 <extra_files type="file" file="out8.ibd" name="ibd" compare="sim_size"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
545 </output>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
546 </test>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 </tests>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548 <help>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 <![CDATA[
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551 @CARDINAL_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553 -----
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555 This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
556
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557 @MSIDATA_INPUT_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
559 - Optional file with pixel coordinates and annotation:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
560
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
561 - Tabular file: One column with x values, one column with y values
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
562 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
563 - Pixel with coordinates outside the coordinates of the input file are ignored
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
564
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
565 ::
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
566
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
567 x_coord y_coord
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
568 1 1
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
569 2 1
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
570 3 1
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
571 ...
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
572 ...
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574 @MZ_TABULAR_INPUT_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576 **Options**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
578 - Pixel filtering/annotation:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
579
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
580 - Either with a tabular file containing x and y coordinates or by entering x-min, x-max, y-min, y-max manually
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
581 - Pixel that are not present in the dataset are ignored
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
582 - An error occurs if the input for filtering (tabular file, x-range or y-range) contains not a single coordinate that occurs in the input dataset
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
583
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
584
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
585 - m/z feature filtering:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
586
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
587 - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
588 - m/z values that are not present in the dataset are ignored
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
589 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
590
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
591
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
592 - m/z feature removing:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
593
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
594 - Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 **Tips**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598
2
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
599 - m/z feautre filtering with a tabular file:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
600
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
601 - For matching the m/z features of the input dataset are rounded to the number of decimal points of the m/z values from the tabular file. In case the input had more than 4 digits m/z values of dataset and tabular file are rounded to 4 digits.
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
602 - Therefore, it is recommended to use the filtering tool only for m/z features which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool 'Join two files on column allowing a small difference' should be used to find corresponding m/z values, which can then be used for filtering.
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
603
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
604 - Problems to select tabular file:
0c4579390f73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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605
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606 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes)
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609 **Output**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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610
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d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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611 - MSI data as (continuous) imzML file
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58376f5a6319 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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612 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
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615 ]]>
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616 </help>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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617 <expand macro="citations"/>
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618 </tool>