Mercurial > repos > galaxyp > cardinal_filtering

annotate filtering.xml @ 3:9d53f1187afb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
author galaxyp
date Thu, 28 Feb 2019 09:13:57 -0500
parents 1a6924281c24
children b045ba419ac6
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.2">
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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="3.0">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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18 #if str($imzml_output) == "imzml_format":
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19 mkdir $outfile_imzml.files_path &&
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20 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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21 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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22 #end if
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23 echo "imzML file:" > $outfile_imzml &&
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24 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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25 ]]>
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26 </command>
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0
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29 <configfiles>
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30 <configfile name="MSI_subsetting"><![CDATA[
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33 ################################# load libraries and read file #################
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36 library(Cardinal)
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37 library(ggplot2)
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38 library(gridExtra)
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40 @READING_MSIDATA@
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43 ########################### QC numbers ########################
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45 ## Number of features (m/z)
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46 maxfeatures = length(features(msidata))
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47 ## Range m/z
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48 minmz = round(min(mz(msidata)), digits=2)
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49 maxmz = round(max(mz(msidata)), digits=2)
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50 ## Number of spectra (pixels)
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51 pixelcount = length(pixels(msidata))
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52 ## Range x coordinates
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53 minimumx = min(coord(msidata)[,1])
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54 maximumx = max(coord(msidata)[,1])
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55 ## Range y coordinates
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56 minimumy = min(coord(msidata)[,2])
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57 maximumy = max(coord(msidata)[,2])
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58 ## Store features for QC plot
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59 featuresinfile = mz(msidata)
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60
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61 ## Next steps will only run if there are more than 0 pixels/features in the file
0
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2
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63 if (ncol(msidata)>0 & nrow(msidata) >0)
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64 {
0
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65 ###################################### Filtering of pixels #####################
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66 ################################################################################
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68 ############ Pixels in two columns format: x and y in different columns #############
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70 #if str($pixels_cond.pixel_filtering) == "two_columns":
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71 print("two columns")
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73 ## read tabular file
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74 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header,
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75 stringsAsFactors = FALSE)
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76 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)]
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77 input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_")
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78 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
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79 pixelsofinterest = dataset_pixels %in% input_pixels
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80
2
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81 tryCatch(
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82 {
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83 msidata = msidata[,pixelsofinterest]
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84 if (ncol(msidata) == 0)
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85 {
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86 stop(call.=FALSE)
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87 }
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88 },
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89 error=function(cond) {
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90 ## 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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91 message("Error during pixel filtering")
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92 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)")
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93 stop(call.=FALSE)
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94 }
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95 )
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96
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97 ## QC values:
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98 numberpixels = nrow(input_list)
0
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99 validpixels=ncol(msidata)
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100
2
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101 ########### Pixels wihin x and y minima and maxima are kept #################
0
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102
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103 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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104 print("pixel range")
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105
2
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106 ## QC values:
0
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107 numberpixels = "range"
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108 validpixels = "range"
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109
2
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110 tryCatch(
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111 {
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112 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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113 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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114 if (ncol(msidata) == 0)
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115 {
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116 stop(call.=FALSE)
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117 }
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118 },
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119 error=function(cond) {
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120 ## in case one of the ranges was outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
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121 message("Error during pixel filtering")
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122 message("Check that both x and y ranges were inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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123 stop(call.=FALSE)
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124 }
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125 )
1
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126
2
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127 ######################## no pixel filtering ################################
0
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128
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129 #elif str($pixels_cond.pixel_filtering) == "none":
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130 print("no pixel filtering")
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131
2
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132 ## QC values:
0
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133 numberpixels = 0
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134 validpixels = 0
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135
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136 #end if
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137
2
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138 ############################# QC data #####################################
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139
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140 ## dataframe for QC of pixel distribution
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141 position_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
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142 colnames(position_df)[3] = "annotation"
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143 position_df\$annotation = factor(position_df\$annotation)
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144 gc()
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145
0
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146 }else{
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147 print("Inputfile has no intensities > 0")
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148 }
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149
2
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150 ################################# filtering of features ######################
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151 ##############################################################################
0
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152
2
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153 ####################### Keep m/z from tabular file #########################
0
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154
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155 ## feature filtering only when pixels/features/intensities are left
1
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156
2
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157
1
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158 if (ncol(msidata) > 0){
2
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159 if (nrow(msidata) > 0)
1
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160 {
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161
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162 #if str($features_cond.features_filtering) == "features_list":
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163 print("feature list")
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164
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165 ## read tabular file, define starting row, extract and count valid features
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166 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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167 extracted_features = input_features[,$features_cond.feature_column]
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168 numberfeatures = length(extracted_features)
2
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169
1
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170 if (class(extracted_features) == "numeric"){
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171 ### max digits given in the input file will be used to match m/z but the maximum is 4
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172 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE)
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173
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174 if (max_digits >4)
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175 {
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176 max_digits = 4
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177 }
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178
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179 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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180 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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181 validmz = length(unique(featuresofinterest))
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182
1
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183 }else{
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184 validmz = 0
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185 featuresofinterest = 0}
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186
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187 ### filter msidata for valid features
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188
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189 tryCatch(
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190 {
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191 msidata = msidata[featuresofinterest,]
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192 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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193 if (nrow(msidata) == 0)
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194 {
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195 stop(call.=FALSE)
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196 }
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197 },
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198 error=function(cond) {
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199 ## in case all provided m/z values were outside the m/z range
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200 ## tool is stopped to avoid continuing with wrong data
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201 message("Error during m/z filtering")
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202 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)")
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203 stop(call.=FALSE)
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204 }
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205 )
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206
1
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207
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208 ############### features within a given range are kept #####################
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209
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210 #elif str($features_cond.features_filtering) == "features_range":
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211 print("feature range")
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212
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213 numberfeatures = "range"
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214 validmz = "range"
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215
2
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216 tryCatch(
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217 {
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218 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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219 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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220 if (nrow(msidata) == 0)
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221 {
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222 stop(call.=FALSE)
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223 }
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224 },
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225 error=function(cond) {
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226 ## in case all m/z features were outside the dataset leading to zero m/z features, tool is stopped to avoid continuing with wrong data
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227 message("Error during m/z filtering")
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228 message("Check that the entered m/z range is inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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229 stop(call.=FALSE)
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230 }
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231 )
1
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232
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233 ############### Remove m/z from tabular file #########################
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234
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235 #elif str($features_cond.features_filtering) == "remove_features":
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236 print("remove features")
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237
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238 ## read tabular file, define starting row, extract and count valid features
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239 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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240 extracted_features = input_features[,$features_cond.feature_column]
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241 numberfeatures = length(extracted_features)
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242 if (class(extracted_features) == "numeric"){
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243 print("input is numeric")
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244 featuresofinterest = extracted_features
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245 }else{featuresofinterest = 0}
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246
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247 ### Here starts removal of features:
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248 plusminus = $features_cond.removal_plusminus
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249
2
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250 tryCatch(
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251 {
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252 mass_to_remove = numeric()
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253 for (masses in featuresofinterest){
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254 #if str($features_cond.units_removal) == "ppm":
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255 plusminus = masses * $features_cond.removal_plusminus/1000000
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256 #end if
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257 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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258 mass_to_remove = append(mass_to_remove, current_mass)}
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259 msidata= msidata[-mass_to_remove, ]
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260 validmz = numberfeatures - nrow(msidata)
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261 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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262 if (nrow(msidata) == 0)
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263 {
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264 stop(call.=FALSE)
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265 }
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266 },
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267 error=function(cond) {
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268 message("Error during removal of m/z features")
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269 stop(call.=FALSE)
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270 }
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271 )
0
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272
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273
2
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274
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275
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276 ######################## No m/z filtering ##############################
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277
1
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278 #elif str($features_cond.features_filtering) == "none":
0
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279
1
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280 print("no feature filtering")
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281 validmz = 0
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282 numberfeatures = 0
0
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283
1
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284 #end if
0
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285
1
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286 }else{
2
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287 print("Inputfile has no m/z features")
1
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288 numberfeatures = NA
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289 validmz = NA
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290 }
0
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291 }else{
2
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292 print("Inputfile or file filtered for pixels has no pixels")
1
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293 numberfeatures = NA
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294 validmz = NA
0
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295 }
2
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296 gc()
0
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297
2
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298 #################### QC numbers #######################
0
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299
2
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300 ## Number of features (m/z)
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301 maxfeatures2 = length(features(msidata))
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302 ## Range m/z
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303 minmz2 = round(min(mz(msidata)), digits=2)
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304 maxmz2 = round(max(mz(msidata)), digits=2)
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305 ## Number of spectra (pixels)
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306 pixelcount2 = length(pixels(msidata))
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307 ## Range x coordinates
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308 minimumx2 = min(coord(msidata)[,1])
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309 maximumx2 = max(coord(msidata)[,1])
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310 ## Range y coordinates
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311 minimumy2 = min(coord(msidata)[,2])
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312 maximumy2 = max(coord(msidata)[,2])
1
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313
2
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314 properties = c("Number of m/z features",
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315 "Range of m/z values",
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316 "Number of pixels",
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317 "Range of x coordinates",
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318 "Range of y coordinates",
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319 "pixel overview",
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320 "feature overview")
0
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321
2
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322 before = c(paste0(maxfeatures),
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323 paste0(minmz, " - ", maxmz),
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324 paste0(pixelcount),
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325 paste0(minimumx, " - ", maximumx),
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326 paste0(minimumy, " - ", maximumy),
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327 paste0("input pixels: ", numberpixels),
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328 paste0("input mz: ", numberfeatures))
0
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329
2
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330 filtered = c(paste0(maxfeatures2),
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331 paste0(minmz2, " - ", maxmz2),
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332 paste0(pixelcount2),
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333 paste0(minimumx2, " - ", maximumx2),
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334 paste0(minimumy2, " - ", maximumy2),
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335 paste0("valid pixels: ", validpixels),
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336 paste0("valid mz: ", validmz))
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337
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338 property_df = data.frame(properties, before, filtered)
0
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339
2
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340 ########################### PDF QC and MSI output ###########################
0
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341
2
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342 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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343 plot(0,type='n',axes=FALSE,ann=FALSE)
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344 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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345 grid.table(property_df, rows= NULL)
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346
2
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347 ## QC report only when pixels/features are left
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348 if (ncol(msidata)>0 & nrow(msidata) >0)
0
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349 {
1
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350
2
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351 ### visual pixel control
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352
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353 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
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354 geom_tile(height = 1, width=1)+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
355 coord_fixed()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
356 ggtitle("Spatial orientation of filtered pixels")+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
357 theme_bw()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
358 theme(plot.title = element_text(hjust = 0.5))+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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359 theme(legend.position="bottom",legend.direction="vertical")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
360 print(pixel_image)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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361
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
362 ### plot features which are removed
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
363 hist(mz(msidata), xlab="m/z", main="Kept m/z values")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
364 #if str($features_cond.features_filtering) == "none":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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365 print("no difference histogram as no m/z filtering took place")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
366 #else:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
367 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
368 print("No difference in m/z values before and after filtering, no histogram drawn")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
369 }else{
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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370 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")}
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
371 #end if
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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372
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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373 dev.off()
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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374
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
375 ## save msidata as imzML file, will only work if there is at least 1 m/z left
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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376
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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377 #if str($imzml_output) == "imzml_format":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
378 if (maxfeatures2 > 0){
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
379 ## make sure that coordinates are integers
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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380 coord(msidata)\$y = as.integer(coord(msidata)\$y)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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381 coord(msidata)\$x = as.integer(coord(msidata)\$x)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
382 writeImzML(msidata, "out")}
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
383 #elif str($imzml_output) == "rdata_format":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
384 ## save msidata as Rfile
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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385 iData(msidata) = iData(msidata)[]
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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386 save(msidata, file="$outfile_rdata")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
387 #end if
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
388
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
389
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390 }else{
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
391 print("Inputfile or filtered file has no intensities > 0")
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
392 dev.off()
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
393 }
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
394
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395 ]]></configfile>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
396 </configfiles>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
397 <inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
398 <expand macro="reading_msidata"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
399 <conditional name="pixels_cond">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
400 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 <option value="none" selected="True">none</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
402 <option value="two_columns">coordinates from tabular file</option>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 <option value="pixel_range">ranges for x and y (manually)</option>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
405 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 <when value="two_columns">
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
407 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates"
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
408 help="Tabular file with two columns: x values and y values"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
409 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
410 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
411 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
412 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 <when value="pixel_range">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
418 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
419 </conditional>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
420
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
421 <conditional name="features_cond">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 <param name="features_filtering" type="select" label="Select m/z feature filtering option">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
423 <option value="none" selected="True">none</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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424 <option value="features_list">keep m/z (tabular file)</option>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <option value="features_range">m/z range (manually)</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
426 <option value="remove_features">remove m/z (tabular file)</option>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 <when value="features_list">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to keep"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <when value="features_range">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 <when value="remove_features">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to remove"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
438 <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"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 <param name="units_removal" type="select" display="radio" optional ="False" label="units">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440 <option value="ppm" selected="True">ppm</option>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 <option value="Da">Da</option>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 </conditional>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
445 <param name="imzml_output" type="select" display = "radio" optional = "False"
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
446 label="Output format" help= "Choose the output format">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
447 <option value="imzml_format" selected="True">imzML</option>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
448 <option value="rdata_format">RData</option>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
449 </param>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 </inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 <outputs>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
453 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
454 <filter>imzml_output =='imzml_format'</filter>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
455 </data>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
456 <data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
457 <filter>imzml_output == 'rdata_format'</filter>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
458 </data>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 </outputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 <tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 <expand macro="infile_imzml"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 <param name="pixel_filtering" value="pixel_range"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 <param name="min_x_range" value="1"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 <param name="max_x_range" value="20"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 <param name="min_y_range" value="2"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 <param name="max_y_range" value="2"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <param name="features_filtering" value="features_range"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
470 <param name="min_mz" value="350"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 <param name="max_mz" value="500"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
472 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 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
1a6924281c24 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">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
475 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 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"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
477 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 <test>
afb831194a79 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"/>
afb831194a79 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
1a6924281c24 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
afb831194a79 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"/>
afb831194a79 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"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
485 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
487 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
1a6924281c24 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.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
489 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
490 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <expand macro="infile_imzml"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <param name="pixel_filtering" value="pixel_range"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 <param name="min_x_range" value="0"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 <param name="max_x_range" value="10"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 <param name="min_y_range" value="2"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 <param name="max_y_range" value="20"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 <param name="features_filtering" value="features_list"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <param name="feature_column" value="1"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <param name="feature_header" value="0"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
503 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
505 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
506 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
507 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
508 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
511 <expand macro="infile_analyze75"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
512 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
514 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
515 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
516 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
517 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 <conditional name="outputs">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522 <param name="outputs_select" value="no_quality_control"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 </conditional>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
524 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" />
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
526 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
527 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
528 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
529 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 </tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532 <help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 <![CDATA[
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535 @CARDINAL_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 -----
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 @MSIDATA_INPUT_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
543 - Optional file with pixel coordinates and annotation:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
544
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
545 - Tabular file: One column with x values, one column with y values
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
546 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
547 - Pixel with coordinates outside the coordinates of the input file are ignored
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
548
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
549 ::
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
550
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
551 x_coord y_coord
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
552 1 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
553 2 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
554 3 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
555 ...
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
556 ...
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558 @MZ_TABULAR_INPUT_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560 **Options**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
562 - Pixel filtering/annotation:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
563
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
564 - Either with a tabular file containing x and y coordinates or by entering x-min, x-max, y-min, y-max manually
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
565 - Pixel that are not present in the dataset are ignored
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
566 - 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
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
567
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
568
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
569 - m/z feature filtering:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
570
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
571 - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
572 - m/z values that are not present in the dataset are ignored
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
573 - 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
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
574
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
575
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
576 - m/z feature removing:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
577
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
578 - Perturbing m/z features such as matrix contaminants 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
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
581 **Tips**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
582
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
583 - m/z feautre filtering with a tabular file:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
584
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
585 - 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.
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
586 - 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.
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
587
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
588 - Problems to select tabular file:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
589
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
590 - 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)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
591
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
593 **Output**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
595 - MSI data as imzML file or .RData (can be read with the Cardinal package in R)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 - pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599 ]]>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
600 </help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
601 <expand macro="citations"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
602 </tool>