Mercurial > repos > galaxyp > cardinal_filtering

annotate filtering.xml @ 4:b045ba419ac6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:05:42 -0400
parents 1a6924281c24
children 97fdb0ce4dd3
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b045ba419ac6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3">
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2 <description>tool for filtering mass spectrometry imaging data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.3">r-gridextra</requirement>
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8 <requirement type="package" version="3.0">r-ggplot2</requirement>
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9 </expand>
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10 <expand macro="print_version"/>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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14 @INPUT_LINKING@
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15 cat '${MSI_subsetting}' &&
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16 Rscript '${MSI_subsetting}' &&
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18 #if str($imzml_output) == "imzml_format":
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19 mkdir $outfile_imzml.files_path &&
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20 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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21 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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22 #end if
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23 echo "imzML file:" > $outfile_imzml &&
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24 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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25 ]]>
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26 </command>
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0
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29 <configfiles>
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30 <configfile name="MSI_subsetting"><![CDATA[
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33 ################################# load libraries and read file #################
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36 library(Cardinal)
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37 library(ggplot2)
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38 library(gridExtra)
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40 @READING_MSIDATA@
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43 ########################### QC numbers ########################
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45 ## Number of features (m/z)
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46 maxfeatures = length(features(msidata))
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47 ## Range m/z
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48 minmz = round(min(mz(msidata)), digits=2)
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49 maxmz = round(max(mz(msidata)), digits=2)
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50 ## Number of spectra (pixels)
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51 pixelcount = length(pixels(msidata))
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52 ## Range x coordinates
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53 minimumx = min(coord(msidata)[,1])
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54 maximumx = max(coord(msidata)[,1])
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55 ## Range y coordinates
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56 minimumy = min(coord(msidata)[,2])
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57 maximumy = max(coord(msidata)[,2])
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58 ## Store features for QC plot
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59 featuresinfile = mz(msidata)
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60
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61 all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata)))
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62 colnames(all_df)[3] = "annotation"
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63
2
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64 ## Next steps will only run if there are more than 0 pixels/features in the file
0
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66 if (ncol(msidata)>0 & nrow(msidata) >0)
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67 {
0
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68 ###################################### Filtering of pixels #####################
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69 ################################################################################
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71 ############ Pixels in two columns format: x and y in different columns #############
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73 #if str($pixels_cond.pixel_filtering) == "two_columns":
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74 print("two columns")
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75
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76 ## read tabular file
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77 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header,
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78 stringsAsFactors = FALSE)
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79 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)]
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80 input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_")
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81 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
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82 pixelsofinterest = dataset_pixels %in% input_pixels
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83
2
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84 tryCatch(
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85 {
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86 msidata = msidata[,pixelsofinterest]
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87 if (ncol(msidata) == 0)
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88 {
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89 stop(call.=FALSE)
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90 }
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91 },
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92 error=function(cond) {
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93 ## 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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94 message("Error during pixel filtering")
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95 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool)")
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96 stop(call.=FALSE)
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97 }
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98 )
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99
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100 ## QC values:
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101 numberpixels = nrow(input_list)
0
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102 validpixels=ncol(msidata)
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103
2
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104 ########### Pixels wihin x and y minima and maxima are kept #################
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105
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106 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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107 print("pixel range")
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108
2
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109 ## QC values:
0
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110 numberpixels = "range"
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111 validpixels = "range"
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112
2
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113 tryCatch(
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114 {
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115 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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116 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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117 if (ncol(msidata) == 0)
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118 {
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119 stop(call.=FALSE)
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120 }
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121 },
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122 error=function(cond) {
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123 ## in case one of the ranges was outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
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124 message("Error during pixel filtering")
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125 message("Check that both x and y ranges were inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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126 stop(call.=FALSE)
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127 }
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128 )
1
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129
2
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130 ######################## no pixel filtering ################################
0
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131
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132 #elif str($pixels_cond.pixel_filtering) == "none":
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133 print("no pixel filtering")
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134
2
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135 ## QC values:
0
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136 numberpixels = 0
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137 validpixels = 0
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138
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139 #end if
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140
2
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141 ############################# QC data #####################################
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142
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143 ## dataframe for QC of pixel distribution
4
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144
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145 remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
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146 colnames(remaining_df)[3] = "annotation"
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147 position_df = rbind(all_df, remaining_df)
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148 position_df[row.names(unique(position_df[,c("x", "y")])),]
2
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149 position_df\$annotation = factor(position_df\$annotation)
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150 gc()
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151
0
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152 }else{
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153 print("Inputfile has no intensities > 0")
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154 }
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155
2
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156 ################################# filtering of features ######################
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157 ##############################################################################
0
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158
2
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159 ####################### Keep m/z from tabular file #########################
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160
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161 ## feature filtering only when pixels/features/intensities are left
1
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162
2
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163
1
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164 if (ncol(msidata) > 0){
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165 if (nrow(msidata) > 0)
1
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166 {
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167
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168 #if str($features_cond.features_filtering) == "features_list":
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169 print("feature list")
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170
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171 ## read tabular file, define starting row, extract and count valid features
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172 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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173 extracted_features = input_features[,$features_cond.feature_column]
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174 numberfeatures = length(extracted_features)
2
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175
1
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176 if (class(extracted_features) == "numeric"){
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177 ### max digits given in the input file will be used to match m/z but the maximum is 4
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178 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE)
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179
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180 if (max_digits >4)
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181 {
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182 max_digits = 4
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183 }
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184
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185 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)
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186 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]
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187 validmz = length(unique(featuresofinterest))
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188
1
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189 }else{
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190 validmz = 0
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191 featuresofinterest = 0}
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192
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193 ### filter msidata for valid features
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194
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195 tryCatch(
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196 {
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197 msidata = msidata[featuresofinterest,]
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198 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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199 if (nrow(msidata) == 0)
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200 {
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201 stop(call.=FALSE)
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202 }
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203 },
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204 error=function(cond) {
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205 ## in case all provided m/z values were outside the m/z range
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206 ## tool is stopped to avoid continuing with wrong data
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207 message("Error during m/z filtering")
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208 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
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209 stop(call.=FALSE)
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210 }
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211 )
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212
1
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213
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214 ############### features within a given range are kept #####################
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215
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216 #elif str($features_cond.features_filtering) == "features_range":
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217 print("feature range")
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218
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219 numberfeatures = "range"
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220 validmz = "range"
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221
2
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222 tryCatch(
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223 {
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224 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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225 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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226 if (nrow(msidata) == 0)
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227 {
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228 stop(call.=FALSE)
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229 }
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230 },
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231 error=function(cond) {
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232 ## in case all m/z features were outside the dataset leading to zero m/z features, tool is stopped to avoid continuing with wrong data
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233 message("Error during m/z filtering")
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234 message("Check that the entered m/z range is inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields")
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235 stop(call.=FALSE)
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236 }
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237 )
1
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238
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239 ############### Remove m/z from tabular file #########################
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240
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241 #elif str($features_cond.features_filtering) == "remove_features":
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242 print("remove features")
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243
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244 ## read tabular file, define starting row, extract and count valid features
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245 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)
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246 extracted_features = input_features[,$features_cond.feature_column]
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247 numberfeatures = length(extracted_features)
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248 if (class(extracted_features) == "numeric"){
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249 print("input is numeric")
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250 featuresofinterest = extracted_features
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251 }else{featuresofinterest = 0}
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252
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253 ### Here starts removal of features:
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254 plusminus = $features_cond.removal_plusminus
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255
2
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256 tryCatch(
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257 {
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258 mass_to_remove = numeric()
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259 for (masses in featuresofinterest){
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260 #if str($features_cond.units_removal) == "ppm":
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261 plusminus = masses * $features_cond.removal_plusminus/1000000
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262 #end if
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263 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
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264 mass_to_remove = append(mass_to_remove, current_mass)}
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265 msidata= msidata[-mass_to_remove, ]
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266 validmz = numberfeatures - nrow(msidata)
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267 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
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268 if (nrow(msidata) == 0)
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269 {
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270 stop(call.=FALSE)
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271 }
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272 },
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273 error=function(cond) {
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274 message("Error during removal of m/z features")
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275 stop(call.=FALSE)
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276 }
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277 )
0
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278
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279
2
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280
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281
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282 ######################## No m/z filtering ##############################
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283
1
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284 #elif str($features_cond.features_filtering) == "none":
0
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285
1
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286 print("no feature filtering")
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287 validmz = 0
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288 numberfeatures = 0
0
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289
1
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290 #end if
0
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291
1
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292 }else{
2
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293 print("Inputfile has no m/z features")
1
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294 numberfeatures = NA
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295 validmz = NA
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296 }
0
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297 }else{
2
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298 print("Inputfile or file filtered for pixels has no pixels")
1
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299 numberfeatures = NA
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300 validmz = NA
0
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301 }
2
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302 gc()
0
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303
2
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304 #################### QC numbers #######################
0
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305
2
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306 ## Number of features (m/z)
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307 maxfeatures2 = length(features(msidata))
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308 ## Range m/z
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309 minmz2 = round(min(mz(msidata)), digits=2)
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310 maxmz2 = round(max(mz(msidata)), digits=2)
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311 ## Number of spectra (pixels)
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312 pixelcount2 = length(pixels(msidata))
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313 ## Range x coordinates
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314 minimumx2 = min(coord(msidata)[,1])
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315 maximumx2 = max(coord(msidata)[,1])
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316 ## Range y coordinates
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317 minimumy2 = min(coord(msidata)[,2])
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318 maximumy2 = max(coord(msidata)[,2])
1
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319
2
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320 properties = c("Number of m/z features",
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321 "Range of m/z values",
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322 "Number of pixels",
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323 "Range of x coordinates",
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324 "Range of y coordinates",
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325 "pixel overview",
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326 "feature overview")
0
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327
2
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328 before = c(paste0(maxfeatures),
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329 paste0(minmz, " - ", maxmz),
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330 paste0(pixelcount),
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331 paste0(minimumx, " - ", maximumx),
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332 paste0(minimumy, " - ", maximumy),
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333 paste0("input pixels: ", numberpixels),
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334 paste0("input mz: ", numberfeatures))
0
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335
2
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336 filtered = c(paste0(maxfeatures2),
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337 paste0(minmz2, " - ", maxmz2),
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338 paste0(pixelcount2),
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339 paste0(minimumx2, " - ", maximumx2),
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340 paste0(minimumy2, " - ", maximumy2),
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341 paste0("valid pixels: ", validpixels),
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342 paste0("valid mz: ", validmz))
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343
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344 property_df = data.frame(properties, before, filtered)
0
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345
2
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346 ########################### PDF QC and MSI output ###########################
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347
2
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348 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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349 plot(0,type='n',axes=FALSE,ann=FALSE)
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350 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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351 grid.table(property_df, rows= NULL)
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352
2
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353 ## QC report only when pixels/features are left
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354 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
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355 {
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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356
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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357 ### visual pixel control
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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358
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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359 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
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360 geom_tile(height = 1, width=1)+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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361 coord_fixed()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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362 ggtitle("Spatial orientation of filtered pixels")+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
363 theme_bw()+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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364 theme(plot.title = element_text(hjust = 0.5))+
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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365 theme(legend.position="bottom",legend.direction="vertical")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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366 print(pixel_image)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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367
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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368 ### plot features which are removed
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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369 hist(mz(msidata), xlab="m/z", main="Kept m/z values")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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370 #if str($features_cond.features_filtering) == "none":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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371 print("no difference histogram as no m/z filtering took place")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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372 #else:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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373 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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374 print("No difference in m/z values before and after filtering, no histogram drawn")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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375 }else{
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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376 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")}
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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377 #end if
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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378
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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379 dev.off()
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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380
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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381 ## save msidata as imzML file, will only work if there is at least 1 m/z left
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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382
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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383 #if str($imzml_output) == "imzml_format":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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384 if (maxfeatures2 > 0){
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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385 ## make sure that coordinates are integers
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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386 coord(msidata)\$y = as.integer(coord(msidata)\$y)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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387 coord(msidata)\$x = as.integer(coord(msidata)\$x)
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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388 writeImzML(msidata, "out")}
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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389 #elif str($imzml_output) == "rdata_format":
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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390 ## save msidata as Rfile
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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391 iData(msidata) = iData(msidata)[]
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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392 save(msidata, file="$outfile_rdata")
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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393 #end if
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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394
1
ee1a5c6c25c7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
395
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
396 }else{
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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397 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
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398 dev.off()
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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399 }
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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400
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
401 ]]></configfile>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
402 </configfiles>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
403 <inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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404 <expand macro="reading_msidata"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
405 <conditional name="pixels_cond">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
406 <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
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407 <option value="none" selected="True">none</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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408 <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
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diff changeset
409 <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
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diff changeset
410 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
411 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
412 <when value="two_columns">
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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413 <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
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414 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
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415 <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
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diff changeset
416 <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
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417 <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
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diff changeset
418 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
419 <when value="pixel_range">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
420 <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
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diff changeset
421 <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
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diff changeset
422 <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
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diff changeset
423 <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
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diff changeset
424 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
425 </conditional>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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426
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
427 <conditional name="features_cond">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
428 <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
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429 <option value="none" selected="True">none</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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430 <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
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diff changeset
431 <option value="features_range">m/z range (manually)</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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432 <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
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diff changeset
433 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
434 <when value="none"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
435 <when value="features_list">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
436 <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
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diff changeset
437 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
438 <when value="features_range">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
439 <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
440 <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
441 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442 <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
443 <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
444 <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
445 <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
446 <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
447 <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
448 </param>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 </when>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 </conditional>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
451 <param name="imzml_output" type="select" display = "radio" optional = "False"
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
452 label="Output format" help= "Choose the output format">
4
b045ba419ac6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
453 <option value="imzml_format" >imzML</option>
b045ba419ac6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
454 <option value="rdata_format" selected="True" >RData</option>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
455 </param>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 </inputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 <outputs>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
459 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
460 <filter>imzml_output =='imzml_format'</filter>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 </data>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
462 <data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
463 <filter>imzml_output == 'rdata_format'</filter>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
464 </data>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${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
466 </outputs>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 <tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <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
470 <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
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 <param name="max_mz" value="500"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
478 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 <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
480 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
481 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
482 <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
483 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 </test>
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="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
488 <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
489 <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
490 <param name="column_y" value="3"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
491 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <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
493 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
494 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
495 <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
496 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 <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
500 <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
501 <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
502 <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
503 <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
504 <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
505 <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
506 <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
507 <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
508 <param name="feature_header" value="0"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
509 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 <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
511 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
512 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
513 <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
514 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517 <expand macro="infile_analyze75"/>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
518 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 <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
520 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
521 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
522 <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
523 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 <test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 <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
527 <conditional name="outputs">
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 <param name="outputs_select" value="no_quality_control"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 </conditional>
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
530 <param name="imzml_output" value="imzml_format"/>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 <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
532 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
533 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="4"/>
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
534 <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
535 </output>
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 </test>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 </tests>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 <help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 <![CDATA[
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 @CARDINAL_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543 -----
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545 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
546
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 @MSIDATA_INPUT_DESCRIPTION@
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
549 - 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
550
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
551 - 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
552 - 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
553 - 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
554
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
555 ::
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
556
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
557 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
558 1 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
559 2 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
560 3 1
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
561 ...
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
562 ...
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564 @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
565
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 **Options**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
568 - 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
569
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
570 - 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
571 - 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
572 - 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
573
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
574
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
575 - 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
576
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
577 - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
578 - m/z values that are not present in the dataset are ignored
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
579 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
580
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
581
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
582 - m/z feature removing:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
583
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
584 - Perturbing m/z features such as matrix contaminants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
585
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
586
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
587 **Tips**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
588
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
589 - m/z feautre filtering with a tabular file:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
590
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
591 - For matching the m/z features of the input dataset are rounded to the number of decimal points of the m/z values from the tabular file. In case the input had more than 4 digits m/z values of dataset and tabular file are rounded to 4 digits.
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
592 - Therefore, it is recommended to use the filtering tool only for m/z features which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool 'Join two files on column allowing a small difference' should be used to find corresponding m/z values, which can then be used for filtering.
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
593
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
594 - Problems to select tabular file:
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
595
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
596 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes)
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599 **Output**
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
600
2
1a6924281c24 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
601 - MSI data as imzML file or .RData (can be read with the Cardinal package in R)
4
b045ba419ac6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
602 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
0
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
603
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
604
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
605 ]]>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
606 </help>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607 <expand macro="citations"/>
afb831194a79 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 </tool>