Mercurial > repos > galaxyp > cardinal_filtering

annotate filtering.xml @ 6:97fdb0ce4dd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author galaxyp
date Wed, 25 Mar 2020 09:24:18 +0000
parents b045ba419ac6
children 5aaea231da6b
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97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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1 <tool id="cardinal_filtering" name="MSI filtering" version="2.4.0.0">
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2 <description>tool for filtering mass spectrometry imaging data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.4.0">bioconductor-cardinal</requirement>
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8 <requirement type="package" version="3.6.1">r-base</requirement>
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9 <requirement type="package" version="2.3">r-gridextra</requirement>
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10 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
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11 </requirements>
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12 <expand macro="print_version"/>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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16 @INPUT_LINKING@
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17 cat '${MSI_subsetting}' &&
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18 Rscript '${MSI_subsetting}' &&
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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 echo "imzML file:" > $outfile_imzml &&
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23 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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24 ]]>
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25 </command>
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28 <configfiles>
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29 <configfile name="MSI_subsetting"><![CDATA[
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32 ################################# load libraries and read file #################
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35 library(Cardinal)
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36 library(ggplot2)
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37 library(gridExtra)
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41 ## function to read RData files independent of filename
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42 loadRData <- function(fileName){
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43 load(fileName)
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44 get(ls()[ls() != "fileName"])
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45 }
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47 #if $infile.ext == 'imzml'
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48 #if str($processed_cond.processed_file) == "processed":
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49 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
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50 centroided(msidata) = $centroids
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51 #else
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52 msidata <- readImzML('infile', attach.only=TRUE)
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53 centroided(msidata) = $centroids
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54 #end if
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55 #elif $infile.ext == 'analyze75'
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56 msidata = readAnalyze('infile', attach.only=TRUE)
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57 centroided(msidata) = $centroids
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58 #else
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59 msidata = loadRData('infile.RData')
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60 msidata = as(msidata, "MSImagingExperiment")
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61 #end if
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64 ########################### QC numbers ########################
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66 ## Number of features (m/z)
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67 maxfeatures = nrow(msidata)
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68 ## Range m/z
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69 minmz = round(min(mz(msidata)), digits=2)
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70 maxmz = round(max(mz(msidata)), digits=2)
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71 ## Number of spectra (pixels)
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72 pixelcount = ncol(msidata)
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73 ## Range x coordinates
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74 minimumx = min(coord(msidata)\$x)
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75 maximumx = max(coord(msidata)\$x)
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76 ## Range y coordinates
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77 minimumy = min(coord(msidata)\$y)
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78 maximumy = max(coord(msidata)\$y)
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79 ## Store features for QC plot
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80 featuresinfile = mz(msidata)
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81
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82 all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata)))
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83 colnames(all_df) = c("x", "y", "annotation")
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84
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85 ## Next steps will only run if there are more than 0 pixels/features in the file
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86
2
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87 if (ncol(msidata)>0 & nrow(msidata) >0)
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88 {
0
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89 ###################################### Filtering of pixels #####################
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90 ################################################################################
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91
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92 ############ Pixels in two columns format: x and y in different columns #############
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93
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94 #if str($pixels_cond.pixel_filtering) == "two_columns":
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95 print("two columns")
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96
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97 ## read tabular file
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98 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header,
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99 stringsAsFactors = FALSE)
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100 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)]
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101 input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_")
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102 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
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103 pixelsofinterest = dataset_pixels %in% input_pixels
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104
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105 tryCatch(
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106 {
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107 msidata = msidata[,pixelsofinterest]
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108 if (ncol(msidata) == 0)
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109 {
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110 stop(call.=FALSE)
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111 }
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112 },
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113 error=function(cond) {
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114 ## 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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115 message("Error during pixel filtering")
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116 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool")
2
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117 stop(call.=FALSE)
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118 }
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119 )
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120
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121 ## QC values:
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122 numberpixels = nrow(input_list)
0
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123 validpixels=ncol(msidata)
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124
2
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125 ########### Pixels wihin x and y minima and maxima are kept #################
0
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126
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127 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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128 print("pixel range")
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129
2
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130 ## QC values:
0
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131 numberpixels = "range"
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132 validpixels = "range"
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133
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134 tryCatch(
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135 {
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136 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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137 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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138 if (ncol(msidata) == 0)
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139 {
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140 stop(call.=FALSE)
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141 }
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142 },
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143 error=function(cond) {
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144 ## in case one of the ranges was outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
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145 message("Error during pixel filtering")
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146 message("Check that both x and y ranges were inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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147 stop(call.=FALSE)
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148 }
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149 )
1
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150
2
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151 ######################## no pixel filtering ################################
0
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152
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153 #elif str($pixels_cond.pixel_filtering) == "none":
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154 print("no pixel filtering")
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155
2
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156 ## QC values:
0
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157 numberpixels = 0
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158 validpixels = 0
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159
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160 #end if
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161
2
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162 ############################# QC data #####################################
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163
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164 ## dataframe for QC of pixel distribution
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165
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166 remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata)))
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167 colnames(remaining_df) = c("x", "y", "annotation")
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168 position_df = rbind(all_df, remaining_df)
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169 position_df[row.names(unique(position_df[,c("x", "y")])),]
2
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170 position_df\$annotation = factor(position_df\$annotation)
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171 gc()
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172
0
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173 }else{
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174 print("Inputfile has no intensities > 0")
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175 }
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176
2
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177 ################################# filtering of features ######################
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178 ##############################################################################
0
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179
2
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180 ####################### Keep m/z from tabular file #########################
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181
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182 ## feature filtering only when pixels/features/intensities are left
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183
2
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184
1
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185 if (ncol(msidata) > 0){
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186 if (nrow(msidata) > 0)
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187 {
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188
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189 #if str($features_cond.features_filtering) == "features_list":
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190 print("feature list")
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191
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192 ## read tabular file, define starting row, extract and count valid features
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193 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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194 extracted_features = input_features[,$features_cond.feature_column]
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195 numberfeatures = length(extracted_features)
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196
1
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197 if (class(extracted_features) == "numeric"){
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198 ### max digits given in the input file will be used to match m/z but the maximum is 4
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199 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE)
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200
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201 if (max_digits >4)
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202 {
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203 max_digits = 4
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204 }
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205
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206 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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207 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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208 validmz = length(unique(featuresofinterest))
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209
1
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210 }else{
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211 validmz = 0
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212 featuresofinterest = 0}
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213
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214 ### filter msidata for valid features
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215
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216 tryCatch(
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217 {
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218 msidata = msidata[featuresofinterest,]
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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 provided m/z values were outside the m/z range
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227 ## tool is stopped to avoid continuing with wrong data
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228 message("Error during m/z filtering")
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229 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
2
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230 stop(call.=FALSE)
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231 }
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232 )
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233
1
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234
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235 ############### features within a given range are kept #####################
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236
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237 #elif str($features_cond.features_filtering) == "features_range":
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238 print("feature range")
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239
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240 numberfeatures = "range"
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241 validmz = "range"
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242
2
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243 tryCatch(
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244 {
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245 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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246 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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247 if (nrow(msidata) == 0)
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248 {
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249 stop(call.=FALSE)
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250 }
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251 },
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252 error=function(cond) {
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253 ## in case all m/z features were outside the dataset leading to zero m/z features, tool is stopped to avoid continuing with wrong data
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254 message("Error during m/z filtering")
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255 message("Check that the entered m/z range is inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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256 stop(call.=FALSE)
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257 }
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258 )
1
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259
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260 ############### Remove m/z from tabular file #########################
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261
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262 #elif str($features_cond.features_filtering) == "remove_features":
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263 print("remove features")
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264
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265 ## read tabular file, define starting row, extract and count valid features
2
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266 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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267 extracted_features = input_features[,$features_cond.feature_column]
1
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268 numberfeatures = length(extracted_features)
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269 if (class(extracted_features) == "numeric"){
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270 print("input is numeric")
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271 featuresofinterest = extracted_features
2
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272 }else{featuresofinterest = 0}
1
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273
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274 ### Here starts removal of features:
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275 plusminus = $features_cond.removal_plusminus
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276
2
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277 tryCatch(
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278 {
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279 mass_to_remove = numeric()
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280 for (masses in featuresofinterest){
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281 #if str($features_cond.units_removal) == "ppm":
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282 plusminus = masses * $features_cond.removal_plusminus/1000000
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283 #end if
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284 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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285 mass_to_remove = append(mass_to_remove, current_mass)}
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286 mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove)
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287
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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288 msidata= msidata[mass_to_keep, ]
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289 validmz = maxfeatures - nrow(msidata)
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290
2
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291 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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292 if (nrow(msidata) == 0)
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293 {
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294 stop(call.=FALSE)
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295 }
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296 },
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297 error=function(cond) {
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298 message("Error during removal of m/z features")
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299 stop(call.=FALSE)
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300 }
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301 )
0
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302
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303
2
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304
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305 ######################## No m/z filtering ##############################
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306
1
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307 #elif str($features_cond.features_filtering) == "none":
0
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308
1
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309 print("no feature filtering")
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310 validmz = 0
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311 numberfeatures = 0
0
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312
1
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313 #end if
0
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314
1
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315 }else{
2
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316 print("Inputfile has no m/z features")
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317 numberfeatures = NA
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318 validmz = NA
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319 }
0
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320 }else{
2
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321 print("Inputfile or file filtered for pixels has no pixels")
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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322 numberfeatures = NA
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323 validmz = NA
0
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324 }
2
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325 gc()
0
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326
2
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327 #################### QC numbers #######################
0
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328
2
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329 ## Number of features (m/z)
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330 maxfeatures2 = nrow(msidata)
2
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331 ## Range m/z
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332 minmz2 = round(min(mz(msidata)), digits=2)
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333 maxmz2 = round(max(mz(msidata)), digits=2)
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334 ## Number of spectra (pixels)
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97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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335 pixelcount2 = ncol(msidata)
2
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336 ## Range x coordinates
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337 minimumx2 = min(coord(msidata)\$x)
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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338 maximumx2 = max(coord(msidata)\$x)
2
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339 ## Range y coordinates
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97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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340 minimumy2 = min(coord(msidata)\$y)
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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341 maximumy2 = max(coord(msidata)\$y)
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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342
2
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343 properties = c("Number of m/z features",
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344 "Range of m/z values",
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345 "Number of pixels",
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346 "Range of x coordinates",
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347 "Range of y coordinates",
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348 "pixel overview",
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349 "feature overview")
0
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350
2
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351 before = c(paste0(maxfeatures),
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diff changeset
352 paste0(minmz, " - ", maxmz),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
353 paste0(pixelcount),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
354 paste0(minimumx, " - ", maximumx),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
355 paste0(minimumy, " - ", maximumy),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
356 paste0("input pixels: ", numberpixels),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
357 paste0("input mz: ", numberfeatures))
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
359 filtered = c(paste0(maxfeatures2),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
360 paste0(minmz2, " - ", maxmz2),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
361 paste0(pixelcount2),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
362 paste0(minimumx2, " - ", maximumx2),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
363 paste0(minimumy2, " - ", maximumy2),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
364 paste0("valid pixels: ", validpixels),
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
365 paste0("valid mz: ", validmz))
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
366
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
367 property_df = data.frame(properties, before, filtered)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
368
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
369 ########################### PDF QC and MSI output ###########################
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
370
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
371 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
372 plot(0,type='n',axes=FALSE,ann=FALSE)
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
373 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier"))
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
374 grid.table(property_df, rows= NULL)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
376 ## QC report only when pixels/features are left
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
377 if (ncol(msidata)>0 & nrow(msidata) >0)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
378 {
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
379
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
380 ### visual pixel control
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
381
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
382 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
383 geom_tile(height = 1, width=1)+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
384 coord_fixed()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
385 ggtitle("Spatial orientation of filtered pixels")+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
386 theme_bw()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
387 theme(plot.title = element_text(hjust = 0.5))+
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
388 theme(legend.position="bottom",legend.direction="vertical")+
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
389 guides(fill=guide_legend(ncol=5,byrow=TRUE))
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
390 print(pixel_image)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
391
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
392
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
393 ### visual mz feature control
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
394
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
395 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
396 colnames(kept_df) = c("mz", "legend")
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
397
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
398 mz_removed = setdiff(featuresinfile, mz(msidata))
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
399 removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed)))
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
400 colnames(removed_df) = c("mz", "legend")
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
401 histogram_df = rbind(removed_df,kept_df)
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
402
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
403 histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) +
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
404 geom_histogram()+ theme_bw()+
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
405 theme(plot.title = element_text(hjust = 0.5))+
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
406 theme(legend.position="bottom",legend.direction="vertical")+
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
407 labs(title="Overview of filtered m/z", x="m/z", y = "count") +
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
408 guides(fill=guide_legend(ncol=5,byrow=TRUE))
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
409 print(histogram_mz)
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
410
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
411
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
412 dev.off()
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
414 ## 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
galaxyp
parents:
diff changeset
415
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
416 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
417 ## make sure that coordinates are integers
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
418 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
parents: 1
diff changeset
419 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
parents: 1
diff changeset
420 writeImzML(msidata, "out")}
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
422
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 }else{
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 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
parents:
diff changeset
425 dev.off()
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 }
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
427
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 ]]></configfile>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 </configfiles>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 <inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 <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
432 <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
433 <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
434 <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
435 <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
436 <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
437 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 <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
440 <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
441 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
442 <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
443 <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
444 <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
parents:
diff changeset
445 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446 <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
447 <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
448 <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
449 <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
450 <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
parents:
diff changeset
451 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 </conditional>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 <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
455 <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
parents:
diff changeset
456 <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
457 <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
458 <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
parents: 1
diff changeset
459 <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
460 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 <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
463 <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
464 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 <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
466 <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
467 <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
468 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <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
470 <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
parents:
diff changeset
471 <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
472 <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
473 <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
474 <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
475 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 </conditional>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 </inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 <outputs>
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
481 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${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
483 </outputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <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
487 <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
488 <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
489 <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
490 <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
491 <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
492 <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
493 <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
494 <param name="max_mz" value="500"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 <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
496 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size">
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
497 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="6"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
498 <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
499 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <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
503 <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
504 <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
505 <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
506 <param name="column_y" value="3"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 <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
508 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
509 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="6"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
510 <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
511 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 <param name="feature_header" value="0"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 <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
525 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
526 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="6"/>
2
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="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
528 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 </test>
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 <expand macro="infile_analyze75"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532 <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
533 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
534 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="6"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
535 <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
536 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 <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
540 <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
541 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
542 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="6"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
543 <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
544 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545 </test>
6
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
546 <test>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
547 <expand macro="processed_infile_imzml"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
548 <conditional name="processed_cond">
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
549 <param name="processed_file" value="processed"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
550 <param name="accuracy" value="100"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
551 <param name="units" value="ppm"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
552 </conditional>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
553 <param name="pixel_filtering" value="two_columns"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
554 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
555 <param name="column_x" value="1"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
556 <param name="column_y" value="3"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
557 <param name="features_filtering" value="remove_features"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
558 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
559 <param name="feature_column" value="1"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
560 <param name="feature_header" value="0"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
561 <param name="removal_plusminus" value="100"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
562 <param name="units_removal" value="ppm"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
563 <output name="QC_overview" file="imzml_filtered8.pdf" compare="sim_size"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
564 <output name="outfile_imzml" ftype="imzml" file="out8.imzml.txt" compare="sim_size">
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
565 <extra_files type="file" file="out8.imzml" name="imzml" lines_diff="6"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
566 <extra_files type="file" file="out8.ibd" name="ibd" compare="sim_size"/>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
567 </output>
97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
568 </test>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 </tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 <help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571 <![CDATA[
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 @CARDINAL_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575 -----
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577 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
578
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579 @MSIDATA_INPUT_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
581 - 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
582
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
583 - 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
584 - 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
585 - 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
586
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
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
589 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
590 1 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
591 2 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
592 3 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
593 ...
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
594 ...
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 @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
597
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598 **Options**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
600 - 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
601
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
602 - 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
603 - 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
604 - 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
605
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
606
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
607 - 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
608
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
609 - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually
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610 - m/z values that are not present in the dataset are ignored
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611 - 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
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612
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613
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614 - m/z feature removing:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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615
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97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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616 - Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
0
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617
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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618
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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619 **Tips**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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620
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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621 - 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
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622
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623 - 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
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624 - 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
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625
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626 - Problems to select tabular file:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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627
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628 - 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
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629
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630
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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631 **Output**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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632
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97fdb0ce4dd3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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633 - MSI data as (continuous) imzML file
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634 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
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635
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636
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637 ]]>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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638 </help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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639 <expand macro="citations"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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640 </tool>