Mercurial > repos > galaxyp > cardinal_filtering

annotate filtering.xml @ 1:aac805a9d2ae draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:25:13 -0400
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aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.1">
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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 $imzml_output:
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19 mkdir $outfile_imzml.files_path &&
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20 ls -l &&
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21 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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22 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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23 #end if
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24 echo "imzML file:" > $outfile_imzml &&
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25 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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28 ]]>
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29 </command>
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32 <configfiles>
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33 <configfile name="MSI_subsetting"><![CDATA[
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36 ################################# load libraries and read file #################
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39 library(Cardinal)
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40 library(ggplot2)
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41 library(gridExtra)
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43 @READING_MSIDATA@
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46 ########################### QC numbers ########################
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47
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48 ## Number of features (m/z)
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49 maxfeatures = length(features(msidata))
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50 ## Range m/z
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51 minmz = round(min(mz(msidata)), digits=2)
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52 maxmz = round(max(mz(msidata)), digits=2)
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53 ## Number of spectra (pixels)
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54 pixelcount = length(pixels(msidata))
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55 ## Range x coordinates
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56 minimumx = min(coord(msidata)[,1])
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57 maximumx = max(coord(msidata)[,1])
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58 ## Range y coordinates
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59 minimumy = min(coord(msidata)[,2])
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60 maximumy = max(coord(msidata)[,2])
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61 ## Number of intensities > 0
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62 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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63 ## Spectra multiplied with m/z (potential number of peaks)
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64 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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65 ## Percentage of intensities > 0
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66 percpeaks = round(npeaks/numpeaks*100, digits=2)
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67 ## Number of empty TICs
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68 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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69 NumemptyTIC = sum(TICs == 0)
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70 ## median TIC
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71 medint = round(median(TICs), digits=2)
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72 ## Store features for QC plot
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73 featuresinfile = mz(msidata)
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75 ## Next steps will only run if there are more than 0 intensities/pixels/features in the file
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77 if (sum(spectra(msidata)[]>0, na.rm=TRUE) > 0)
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78 {
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81 ## prepare dataframe for QC of pixel distribution (will be overwritten in filtering of pixels condition)
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82 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))
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83 colnames(position_df)[3] = "annotation"
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84
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85 ###################################### Filtering of pixels #####################
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86 ################################################################################
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87
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88 ############ Pixels in two columns format: x and y in different columns #############
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89
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90 #if str($pixels_cond.pixel_filtering) == "two_columns":
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91 print("two columns")
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92
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93 ## read tabular file
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94 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header,
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95 stringsAsFactors = FALSE)
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96 numberpixels = nrow(input_list)
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97 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y, $pixels_cond.column_names)]
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98
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99 ## rewrite into x = 1, y = 1 format and filter msidata, count validpixels
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100 pixelvector = character()
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101 for (pixel in 1:nrow(inputpixels)){
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102 pixelvector[pixel] = paste0("x = ", inputpixels[pixel,1],", ", "y = ", inputpixels[pixel,2])}
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103 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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104 msidata = msidata[,pixelsofinterest]
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105 validpixels=ncol(msidata)
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106
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107 ## in case some pixels are left print annotation plot
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108 colnames(inputpixels) = c("x", "y", "annotation")
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109 position_df = merge(coord(msidata)[,1:2], inputpixels, by=c("x", "y"), all.x=TRUE)
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110 colnames(position_df)[3] = "annotation"
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111 position_df\$annotation = factor(position_df\$annotation)
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112
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113
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114 ########### Pixels wihin x and y minima and maxima are kept ###################
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115
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116 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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117 print("pixel range")
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118
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119 numberpixels = "range"
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120 validpixels = "range"
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121
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122 ## only filter pixels if at least one pixel will be left
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123 if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0 & sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0){
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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124
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125 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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126 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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127 }else{
1
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128
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129 print("no valid pixel found")
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130 msidata = msidata[,0]}
0
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131
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132 ## update position_df for filtered pixels
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133 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))
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134 colnames(position_df)[3] = "annotation"
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135 position_df\$annotation = factor(position_df\$annotation)
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136
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137 #elif str($pixels_cond.pixel_filtering) == "none":
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138 print("no pixel filtering")
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139
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140 numberpixels = 0
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141 validpixels = 0
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142
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143 #end if
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144
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145 }else{
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146 print("Inputfile has no intensities > 0")
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147 }
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148
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149 ################################# filtering of features ######################
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150 ##############################################################################
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151
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152 ####################### Keep m/z from tabular file #########################
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153
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154 ## feature filtering only when pixels/features/intensities are left
1
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155
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156 if (ncol(msidata) > 0){
0
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157 npeaks_before_filtering= sum(spectra(msidata)[]>0, na.rm=TRUE)
1
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158 if (npeaks_before_filtering > 0)
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159 {
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160
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161 #if str($features_cond.features_filtering) == "features_list":
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162 print("feature list")
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163
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164 ## read tabular file, define starting row, extract and count valid features
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165 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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166 extracted_features = input_features[,$features_cond.feature_column]
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167 numberfeatures = length(extracted_features)
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168 if (class(extracted_features) == "numeric"){
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169 ### max digits given in the input file will be used to match m/z but the maximum is 4
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170 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE)
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171
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172 if (max_digits >4)
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173 {
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174 max_digits = 4
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175 }
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176
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177 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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178 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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179 validmz = length(unique(featuresofinterest))
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180 }else{
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181 validmz = 0
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182 featuresofinterest = 0}
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183
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184 ### filter msidata for valid features
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185 msidata = msidata[featuresofinterest,]
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186
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187 ############### features within a given range are kept #####################
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188
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189 #elif str($features_cond.features_filtering) == "features_range":
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190 print("feature range")
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191
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192 numberfeatures = "range"
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193 validmz = "range"
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194
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195 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){
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196 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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197 }else{
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198 msidata = msidata[0,]
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199 print("no valid mz range")}
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200
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201 ############### Remove m/z from tabular file #########################
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202
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203 #elif str($features_cond.features_filtering) == "remove_features":
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204 print("remove features")
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205
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206 ## read tabular file, define starting row, extract and count valid features
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207 input_features = read.delim("$mz_tabular", header = $features_cond.removal_header, stringsAsFactors = FALSE)
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208 extracted_features = input_features[,$features_cond.removal_column]
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209 numberfeatures = length(extracted_features)
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210 if (class(extracted_features) == "numeric"){
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211 print("input is numeric")
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212 featuresofinterest = extracted_features
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213 validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata)))
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214 }else{featuresofinterest = 0
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215 validmz = 0}
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216
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217 ### Here starts removal of features:
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218 plusminus = $features_cond.removal_plusminus
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219
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220 mass_to_remove = numeric()
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221 if (sum(featuresofinterest) > 0){
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222 for (masses in featuresofinterest){
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223 #if str($features_cond.units_removal) == "ppm":
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224 plusminus = masses * $features_cond.removal_plusminus/1000000
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225 #end if
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226 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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227 mass_to_remove = append(mass_to_remove, current_mass)}
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228 msidata= msidata[-mass_to_remove, ]
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229 }else{print("No features were removed as they were not fitting to m/z values and/or range")}
0
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230
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231
1
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232 #elif str($features_cond.features_filtering) == "none":
0
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233
1
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234 print("no feature filtering")
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235 validmz = 0
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236 numberfeatures = 0
0
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237
1
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238 #end if
0
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239
1
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240 ## save msidata as Rfile
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241 save(msidata, file="$msidata_filtered")
0
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242
1
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243 ## Number of empty TICs
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244 TICs2 = colSums(spectra(msidata)[], na.rm=TRUE)
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245 ## Number of intensities > 0
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246 npeaks2= sum(spectra(msidata)[]>0, na.rm=TRUE)
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247 ## Spectra multiplied with m/z (potential number of peaks)
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248 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
0
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249
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250
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251
1
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252 }else{
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253 print("Inputfile or file filtered for pixels has no intensities > 0")
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254 numberfeatures = NA
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255 validmz = NA
0
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256 ## Number of empty TICs
1
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257 TICs2 = 0
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258 npeaks2 = 0
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259 numpeaks2 = 0
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260 }
0
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261 }else{
1
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262 print("Inputfile or file filtered for pixels has no pixels left")
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263 numberfeatures = NA
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264 validmz = NA
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265 ## Number of empty TICs
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266 TICs2 = 0
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267 npeaks2 = 0
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268 numpeaks2 = 0
0
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269 }
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270 #################### QC numbers #######################
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271
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272
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273 ## Number of features (m/z)
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274 maxfeatures2 = length(features(msidata))
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275 ## Range m/z
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276 minmz2 = round(min(mz(msidata)), digits=2)
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277 maxmz2 = round(max(mz(msidata)), digits=2)
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278 ## Number of spectra (pixels)
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279 pixelcount2 = length(pixels(msidata))
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280 ## Range x coordinates
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281 minimumx2 = min(coord(msidata)[,1])
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282 maximumx2 = max(coord(msidata)[,1])
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283 ## Range y coordinates
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284 minimumy2 = min(coord(msidata)[,2])
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285 maximumy2 = max(coord(msidata)[,2])
1
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286
0
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287 ## Percentage of intensities > 0
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288 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2)
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289 ## Number of empty TICs
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290 NumemptyTIC2 = sum(TICs2 == 0)
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291 ## median TIC
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292 medint2 = round(median(TICs2), digits=2)
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293
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294 properties = c("Number of m/z features",
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295 "Range of m/z values",
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296 "Number of pixels",
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297 "Range of x coordinates",
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298 "Range of y coordinates",
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299 "Intensities > 0",
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300 "Median TIC per pixel",
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301 "Number of empty spectra",
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302 "pixel overview",
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303 "feature overview")
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304
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305 before = c(paste0(maxfeatures),
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306 paste0(minmz, " - ", maxmz),
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307 paste0(pixelcount),
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308 paste0(minimumx, " - ", maximumx),
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309 paste0(minimumy, " - ", maximumy),
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310 paste0(percpeaks, " %"),
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311 paste0(medint),
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312 paste0(NumemptyTIC),
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313 paste0("input pixels: ", numberpixels),
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314 paste0("input mz: ", numberfeatures))
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315
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316 filtered = c(paste0(maxfeatures2),
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317 paste0(minmz2, " - ", maxmz2),
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318 paste0(pixelcount2),
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319 paste0(minimumx2, " - ", maximumx2),
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320 paste0(minimumy2, " - ", maximumy2),
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321 paste0(percpeaks2, " %"),
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322 paste0(medint2),
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323 paste0(NumemptyTIC2),
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324 paste0("valid pixels: ", validpixels),
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325 paste0("valid mz: ", validmz))
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326
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327 property_df = data.frame(properties, before, filtered)
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328 print(property_df)
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329
1
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330 ########################### PDF QC and imzml output ###########################
0
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331
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332 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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333 plot(0,type='n',axes=FALSE,ann=FALSE)
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334 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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335 grid.table(property_df, rows= NULL)
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336
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337 ## QC report with more than value-table: only when pixels/features/intensities are left
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338 if (npeaks2 > 0)
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339 {
1
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340
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341 ## save msidata as imzML file, will only work if there is at least 1 m/z left
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342 #if $imzml_output:
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343 if (maxfeatures2 > 0){
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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344 writeImzML(msidata, "out")}
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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345 #end if
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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346
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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347
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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348 ### visual pixel control
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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349
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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350 levels(position_df\$annotation) = factor(paste(1:length(levels(position_df\$annotation)), levels(position_df\$annotation), sep="_"))
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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351
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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352 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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353 geom_tile(height = 1, width=1)+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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354 coord_fixed()+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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355 ggtitle("Spatial orientation of filtered pixels")+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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356 theme_bw()+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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357 theme(plot.title = element_text(hjust = 0.5))+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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358 theme(text=element_text(family="ArialMT", face="bold", size=12))+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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359 theme(legend.position="bottom",legend.direction="vertical")+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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360 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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361 guides(fill=guide_legend(ncol=4,byrow=TRUE))
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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362
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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363 coord_labels = aggregate(cbind(x,y)~annotation, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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364 coord_labels\$file_number = 1:length(levels(position_df\$annotation))
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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365
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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366 for(file_count in 1:nrow(coord_labels))
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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367 {pixel_image = pixel_image + annotate("text",x=coord_labels[file_count,"x"],
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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368 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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369
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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370 print(pixel_image)
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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371
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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372 ### control features which are removed
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 hist(mz(msidata), xlab="m/z", main="Kept m/z values")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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374 #if str($features_cond.features_filtering) == "none":
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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375 print("no difference histogram as no m/z filtering took place")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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376 #else:
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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377
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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378 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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379 print("No difference in m/z values before and after filtering, no histogram drawn")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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380 }else{
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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381 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")}
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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382 #end if
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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383
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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384 dev.off()
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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385
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
386
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
387 }else{
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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388 print("Inputfile or filtered file has no intensities > 0")
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
389 dev.off()
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
390 }
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
391 ]]></configfile>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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392 </configfiles>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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393 <inputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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394 <expand macro="reading_msidata"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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395 <conditional name="pixels_cond">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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396 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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397 <option value="none" selected="True">none</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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398 <option value="two_columns">list of pixel coordinates (tabular file)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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399 <option value="pixel_range">ranges for x and y (manually)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
400 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 <when value="none"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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402 <when value="two_columns">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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403 <expand macro="reading_pixel_annotations"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
405 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 <when value="pixel_range">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
408 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
409 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
410 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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411 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
412 </conditional>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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413
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
414 <conditional name="features_cond">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 <param name="features_filtering" type="select" label="Select m/z feature filtering option">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
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416 <option value="none" selected="True">none</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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417 <option value="features_list">keep a list of m/z (tabular file)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418 <option value="features_range">m/z range (manually)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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419 <option value="remove_features">remove a list of m/z (tabular file)</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
420 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421 <when value="none"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 <when value="features_list">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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423 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to keep"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <when value="features_range">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 <when value="remove_features">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to remove"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 <param name="removal_plusminus" type="float" value="20" label="Window in which all m/z will be removed" help="This value is the half window size, it will be added and substracted from the given input value"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <param name="units_removal" type="select" display="radio" optional ="False" label="units">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 <option value="ppm" selected="True">ppm</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 <option value="Da">Da</option>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 </param>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 </when>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
437 </conditional>
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
438 <param name="imzml_output" type="boolean" label="Output of imzML file" truevalue="TRUE" falsevalue="FALSE"/>
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
439
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440 </inputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
442 <outputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 <data format="rdata" name="msidata_filtered" label="${tool.name} on ${on_string}"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
445 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
446 <filter>imzml_output</filter>
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
447 </data>
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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448 </outputs>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 <tests>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 <param name="pixel_filtering" value="pixel_range"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 <param name="min_x_range" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 <param name="max_x_range" value="20"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 <param name="min_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 <param name="max_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457 <param name="features_filtering" value="features_range"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 <param name="min_mz" value="350" />
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 <param name="max_mz" value="500"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 <param name="pixel_filtering" value="two_columns"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 <param name="annotation_file" ftype="tabular" value = "inputpixels_2column.tabular"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 <param name="column_x" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 <param name="column_y" value="3"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <param name="column_names" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size"/>
1
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
472 <!--imzml output test not yet working: output name="outfile_imzml" file="filtering_imzmls/summary" compare="sim_size" delta="10000">
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
473 <extra_files type="file" name="imzml" value="filtering_imzmls/out4.imzML" compare="sim_size" delta="10000"/>
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
474 <extra_files type="file" name="ibd" value="filtering_imzmls/out4.ibd" compare="sim_size" delta="10000"/>
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
475 </output-->
0
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 <expand macro="infile_imzml"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 <param name="pixel_filtering" value="pixel_range"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 <param name="min_x_range" value="0"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
481 <param name="max_x_range" value="10"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 <param name="min_y_range" value="2"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 <param name="max_y_range" value="20"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <param name="features_filtering" value="features_list"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <param name="feature_column" value="1"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 <param name="feature_header" value="0"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" />
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
490 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <expand macro="infile_analyze75"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
494 <output name="msidata_filtered" file="analyze_filteredoutside.RData" compare="sim_size" />
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
495 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 <test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 <conditional name="outputs">
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 <param name="outputs_select" value="no_quality_control"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
500 </conditional>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size"/>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" />
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503 </test>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 </tests>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 <help>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506 <![CDATA[
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 @CARDINAL_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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509
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510 -----
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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511
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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512 This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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513
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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514 @MSIDATA_INPUT_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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515
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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516 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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517
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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518 @MZ_TABULAR_INPUT_DESCRIPTION@
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519
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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520 **Options**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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521
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522 - pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible). Pixel that are not present in the dataset are ignored. It is not possible to filter only for pixels that are not present in the dataset.
aac805a9d2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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523 - m/z feature filtering: m/z values for filtering should be either imported as a tabular file containing containing m/z of interest or by defining a range for the m/z values. m/z that are not present in the dataset are ignored. It is not possible to filter only for m/z that are not present in the dataset.
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a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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524 - m/z feature removing: perturbing m/z features such as matrix contaminants can be removed by specifying their m/z in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed.
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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525
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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526
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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527 **Tips**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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528
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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529 - Numeric m/z features imported via a tabular file and m/z features of the dataset are rounded to 4 decimal points (or maximum number of decimal points of input m/z) and then matched. Therefore, it is recommended to use the filtering tool only for m/z 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.
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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530 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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531
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532
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533 **Output**
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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534
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535 - MSI data as .RData output (can be read with the Cardinal package in R)
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536 - optional: MSI data as imzML file
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537 - pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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538
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539
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540 ]]>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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541 </help>
a2988d8d4b77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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542 <expand macro="citations"/>
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543 </tool>