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annotate msi_filtering.xml @ 1:a170455feb59 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
author galaxyp
date Mon, 23 Apr 2018 17:16:25 -0400
parents 91e2a0c9695c
children bc1ff8d086e3
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a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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1 <tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0.1">
0
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2 <description>tool for filtering mass spectrometry imaging data</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
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5 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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10 #if $infile.ext == 'imzml'
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11 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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12 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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13 #elif $infile.ext == 'analyze75'
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14 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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15 cp '${infile.extra_files_path}/img' infile.img &&
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16 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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17 #else
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18 ln -s $infile infile.RData &&
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19 #end if
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20 cat '${MSI_subsetting}' &&
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21 echo ${MSI_subsetting} &&
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22 Rscript '${MSI_subsetting}'
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24 ]]>
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25 </command>
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26 <configfiles>
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27 <configfile name="MSI_subsetting"><![CDATA[
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91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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30 ################################# load libraries and read file #########################
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91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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33 library(Cardinal)
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34 library(gridExtra)
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36 ## Read MALDI Imaging dataset
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38 #if $infile.ext == 'imzml'
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39 msidata = readMSIData('infile.imzML')
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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40 #elif $infile.ext == 'analyze75'
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41 msidata = readMSIData('infile.hdr')
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42 #else
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43 load('infile.RData')
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44 #end if
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46 ###################################### inputfile properties in numbers ######################
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47
1
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48 #if $outputs.outputs_select == "quality_control":
0
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49 ## Number of features (mz)
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50 maxfeatures = length(features(msidata))
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51 ## Range mz
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52 minmz = round(min(mz(msidata)), digits=2)
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53 maxmz = round(max(mz(msidata)), digits=2)
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54 ## Number of spectra (pixels)
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55 pixelcount = length(pixels(msidata))
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56 ## Range x coordinates
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57 minimumx = min(coord(msidata)[,1])
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58 maximumx = max(coord(msidata)[,1])
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59 ## Range y coordinates
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60 minimumy = min(coord(msidata)[,2])
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61 maximumy = max(coord(msidata)[,2])
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62 ## Number of intensities > 0
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63 npeaks= sum(spectra(msidata)[]>0)
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64 ## Spectra multiplied with mz (potential number of peaks)
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65 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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66 ## Percentage of intensities > 0
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67 percpeaks = round(npeaks/numpeaks*100, digits=2)
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68 ## Number of empty TICs
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69 TICs = colSums(spectra(msidata)[])
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70 NumemptyTIC = sum(TICs == 0)
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71 ## median TIC
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72 medint = round(median(TICs), digits=2)
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73 ## Store features for QC plot
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74 featuresinfile = mz(msidata)
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75 #end if
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76
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78 ###################################### filtering of pixels ######################
1
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80 #if str($pixels_cond.pixel_filtering) == "single_column":
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81 print("single column")
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82
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83 #if $pixels_cond.single_pixels:
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84 input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE)
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85 numberpixels = length(input_list[,$pixels_cond.pixel_column])
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86 valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata))
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87 validpixels = sum(valid_entries)
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88
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89 if (validpixels != 0)
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90 {
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91 pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]
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92 msidata = msidata[,pixelsofinterest]
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93 }else{
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94 validpixels=0
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95 }
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96
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97 #else
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98 validpixels=0
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99 numberpixels = 0
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100 #end if
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101
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102 #elif str($pixels_cond.pixel_filtering) == "two_columns":
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103 print("two columns")
0
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104
1
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105 #if $pixels_cond.two_columns_pixel:
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106
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107 input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE,
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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108 stringsAsFactors = FALSE)
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109 numberpixels = length(input_list[,$pixels_cond.pixel_column_x])
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110
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111 inputpixel_x = input_list[,$pixels_cond.pixel_column_x]
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112 inputpixel_y = input_list[,$pixels_cond.pixel_column_y]
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113
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114 inputpixels = cbind(inputpixel_x, inputpixel_y)
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115 colnames(inputpixels) = c("x", "y")
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116 valid_rows = merge(inputpixels, coord(msidata)[,1:2])
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117 validpixels = nrow(valid_rows)
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118
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119 if (validpixels != 0)
0
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120 {
1
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121
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122 pixelvector = character()
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123
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124 for (pixel in 1:nrow(valid_rows))
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125 {
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126 pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])
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127 }
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128
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129 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]
0
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130 msidata = msidata[,pixelsofinterest]
1
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131 }else{
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132 validpixels=0
0
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133 }
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134
1
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135
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136 #else
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137 validpixels=0
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138 numberpixels = 0
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139 #end if
0
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140
1
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141 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
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142 print("pixel range")
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143
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144 numberpixels = "range"
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145 validpixels = "range"
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146
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147 if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0)
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148 {
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149 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
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150 }
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151
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152 if (sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0)
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153 {
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154 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
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155 }
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156
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157
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158
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159 #elif str($pixels_cond.pixel_filtering) == "none":
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160 print("no pixel filtering")
0
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161 numberpixels = 0
1
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162 validpixels = 0
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163
0
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164 #end if
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165
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166
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167
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168 ###################################### filtering of features ######################
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169
1
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170 #if str($features_cond.features_filtering) == "features_list":
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171
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172 print("feature list")
0
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173
1
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174 input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE)
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175
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176 startingrow = $features_cond.feature_header+1
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177 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column]
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178 numberfeatures = length(extracted_features)
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179
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180
1
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181 if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE)
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182
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183 { print("no m/z = in data")
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184
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185 if (class(extracted_features) == "numeric")
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186 {
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187 charactervector = rep("m/z = ", numberfeatures)
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188 mz_added = paste0(charactervector, round(extracted_features,digits=2))
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189 validfeatures = mz_added %in% names(features(msidata))
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190 featuresofinterest = features(msidata)[names(features(msidata)) %in% mz_added[validfeatures]]
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191 }else{
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192 validfeatures = 0
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193 featuresofinterest = features(msidata)
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194 }
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195 }else{
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196 validfeatures = extracted_features %in% names(features(msidata))
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197 featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
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198 }
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199
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200 msidata = msidata[featuresofinterest,]
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201
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202
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203
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204 #elif str($features_cond.features_filtering) == "features_range":
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205
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206 print("feature range")
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207
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208 numberfeatures = "range"
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209 validfeatures = NA
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210
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211 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0)
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212 {
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213 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
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214 }
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215
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216
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217 #elif str($features_cond.features_filtering) == "none":
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218
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219 print("no feature filtering")
0
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220 validfeatures = 0
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221 numberfeatures = 0
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222 #end if
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223
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224
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225
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226 # save msidata as Rfile
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227 save(msidata, file="$msidata_filtered")
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228
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229 ###################################### outputfile properties in numbers ######################
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230
1
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231 #if $outputs.outputs_select == "quality_control":
0
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232
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233 ## Number of features (mz)
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234 maxfeatures2 = length(features(msidata))
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235 ## Range mz
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236 minmz2 = round(min(mz(msidata)), digits=2)
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237 maxmz2 = round(max(mz(msidata)), digits=2)
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238 ## Number of spectra (pixels)
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239 pixelcount2 = length(pixels(msidata))
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240 ## Range x coordinates
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241 minimumx2 = min(coord(msidata)[,1])
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242 maximumx2 = max(coord(msidata)[,1])
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243 ## Range y coordinates
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244 minimumy2 = min(coord(msidata)[,2])
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245 maximumy2 = max(coord(msidata)[,2])
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246 ## Number of intensities > 0
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247 npeaks2= sum(spectra(msidata)[]>0)
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248 ## Spectra multiplied with mz (potential number of peaks)
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249 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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250 ## Percentage of intensities > 0
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251 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2)
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252 ## Number of empty TICs
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253 TICs2 = colSums(spectra(msidata)[])
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254 NumemptyTIC2 = sum(TICs2 == 0)
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255 ## median TIC
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256 medint2 = round(median(TICs2), digits=2)
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257
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258
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259 properties = c("Number of mz features",
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260 "Range of mz values [Da]",
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261 "Number of pixels",
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262 "Range of x coordinates",
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263 "Range of y coordinates",
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264 "Intensities > 0",
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265 "Median TIC per pixel",
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266 "Number of zero TICs",
1
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267 "pixel overview",
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268 "feature overview")
0
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269
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270 before = c(paste0(maxfeatures),
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271 paste0(minmz, " - ", maxmz),
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272 paste0(pixelcount),
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273 paste0(minimumx, " - ", maximumx),
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274 paste0(minimumy, " - ", maximumy),
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275 paste0(percpeaks, " %"),
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276 paste0(medint),
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277 paste0(NumemptyTIC),
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278 paste0("input pixels: ", numberpixels),
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279 paste0("input mz: ", numberfeatures))
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280
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281 filtered = c(paste0(maxfeatures2),
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282 paste0(minmz2, " - ", maxmz2),
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283 paste0(pixelcount2),
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284 paste0(minimumx2, " - ", maximumx2),
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285 paste0(minimumy2, " - ", maximumy2),
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286 paste0(percpeaks2, " %"),
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287 paste0(medint2),
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288 paste0(NumemptyTIC2),
1
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289 paste0("valid pixels: ", validpixels),
0
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290 paste0("valid mz: ", sum(validfeatures)))
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291
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292
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293 property_df = data.frame(properties, before, filtered)
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294
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295
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296
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297 ######################################## PDF QC #############################################
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298
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299 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
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300 plot(0,type='n',axes=FALSE,ann=FALSE)
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301
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302 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
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303
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304
1
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305
0
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306 grid.table(property_df, rows= NULL)
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307
1
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308 ### heatmap image as visual pixel control
0
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309
1
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310 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0)
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311 {
0
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312
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313
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314 image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none",
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315 main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2))
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316
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317 ### control features which are left
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318
1
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319 plot(featuresinfile, rep(1,length(featuresinfile)), yaxt="n", ylab=NA, xlab="m/z values", col="red", ylim=c(0.8, 1.1), main="Distribution of m/z values")
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320 lines(mz(msidata),rep(0.9, length(mz(msidata))), col="green", type="p")
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321 legend("top", horiz=TRUE,
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322 legend = c("before", "filtered"),
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323 fill = c("red", "green"))
0
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324
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325
1
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326
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327
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328 }else{
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329 print("file has no features or pixels left")
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330 }
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331
0
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332 dev.off()
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333
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334 #end if
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335
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336 ######################################## intensity matrix ##################################
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337
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338 #if $output_matrix:
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339
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340 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0)
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341 {
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342
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343 spectramatrix = spectra(msidata)
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344 rownames(spectramatrix) = mz(msidata)
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345 newmatrix = rbind(pixels(msidata), spectramatrix)
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346 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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347
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348 }else{
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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349 print("file has no features or pixels left")
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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350 }
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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351
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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352 #end if
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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353
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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354
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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355 ]]></configfile>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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356 </configfiles>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
357 <inputs>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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358 <param name="infile" type="data" format="imzml, rdata, analyze75"
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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359 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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360 help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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361
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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362 <conditional name="pixels_cond">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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363 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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364 <option value="none" selected="True">none</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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365 <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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366 <option value="two_columns">tabular file with separate columns for x and y values</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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367 <option value="pixel_range">ranges for x and y</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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368 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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369 <when value="none"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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370 <when value="single_column">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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371 <param name="single_pixels" type="data" format="tabular" label="Pixels in single column for filtering of MSI data"
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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372 help="tabular file with pixels of interest in the form x = 1, y = 1"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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373 <param name="pixel_column" data_ref="single_pixels" label="Column with pixels" type="data_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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374 </when>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
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375 <when value="two_columns">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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376 <param name="two_columns_pixel" type="data" format="tabular" label="Pixels in two columns for filtering of MSI data"
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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377 help="tabular file with pixels of interest in two separate columns"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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378 <param name="pixel_column_x" data_ref="two_columns_pixel" label="Column with x values" type="data_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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379 <param name="pixel_column_y" data_ref="two_columns_pixel" label="Column with y values" type="data_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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380 </when>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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381 <when value="pixel_range">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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382 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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383 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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384 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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385 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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386 </when>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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387 </conditional>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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388
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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389 <conditional name="features_cond">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
390 <param name="features_filtering" type="select" label="Select feature filtering option">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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391 <option value="none" selected="True">none</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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392 <option value="features_list">tabular file with features (data type: 800.12 or m/z = 800.12)</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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393 <option value="features_range">range of features</option>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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394 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
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395
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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parents: 0
diff changeset
396 <when value="none"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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397 <when value="features_list">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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398 <param name="inputfeatures" type="data" format="tabular" label="Features for filtering of MSI data" help="tabular file with masses of interest either as numbers (800.05) or in the form m/z = 800.05"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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399 <param name="feature_column" data_ref="inputfeatures" label="Column with features" type="data_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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400 <param name="feature_header" label="Number of header lines to skip" value="0" type="integer"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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401 </when>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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402 <when value="features_range">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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403 <param name="min_mz" type="integer" value="1" label="Minimum value for mz (in Dalton)"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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404 <param name="max_mz" type="integer" value="100" label="Maximum value for mz (in Dalton)"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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405 </when>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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406 </conditional>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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407
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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408 <conditional name="outputs">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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409 <param name="outputs_select" type="select" label="Quality control output">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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410 <option value="quality_control" selected="True">yes</option>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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411 <option value="no_quality_control">no</option>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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412 </param>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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413 <when value="quality_control">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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414 <param name="inputmz" type="float" value="1296.7" label="Mass for which a heatmap image will be drawn" help="Use a mass which is still present in all pixels to control if the pixel filtering went well"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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415 <param name="plusminus_dalton" value="0.25" type="float" label="mass range for mz value" help="plusminus mass window in Dalton"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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416 </when>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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417 <when value="no_quality_control"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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418 </conditional>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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419 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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420 </inputs>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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421 <outputs>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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422 <data format="rdata" name="msidata_filtered" label="${tool.name} ${on_string}"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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423 <data format="pdf" name="filtering_qc" from_work_dir="filtertool_QC.pdf" label = "QC ${tool.name} ${on_string}">
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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424 <filter>outputs["outputs_select"] == "quality_control"</filter>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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425 </data>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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426 <data format="tabular" name="matrixasoutput" label="Matrix ${tool.name} on ${on_string}">
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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427 <filter>output_matrix</filter>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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428 </data>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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429 </outputs>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
430
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
431 <tests>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
432 <test expect_num_outputs="2">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
433 <param name="infile" value="" ftype="imzml">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
434 <composite_data value="Example_Continuous.imzML"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
435 <composite_data value="Example_Continuous.ibd"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
436 </param>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
437 <param name="pixel_filtering" value="single_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
438 <param name="single_pixels" ftype="tabular" value = "inputpixels.tabular"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
439 <param name="pixel_column" value="1"/>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
440 <param name="features_filtering" value="features_list"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
441 <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
442 <param name="feature_column" value="2"/>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
443 <param name="feature_header" value="1"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
444 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
445 <param name="inputmz" value="328.9"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
446 <param name="plusminus_dalton" value="0.25"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
447 <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
448 <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size" />
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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449 </test>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
450 <test expect_num_outputs="2">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
451 <param name="infile" value="" ftype="imzml">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
452 <composite_data value="Example_Continuous.imzML"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
453 <composite_data value="Example_Continuous.ibd"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
454 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
455 <param name="pixel_filtering" value="pixel_range"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
456 <param name="min_x_range" value="0"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
457 <param name="max_x_range" value="10"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
458 <param name="min_y_range" value="2"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
459 <param name="max_y_range" value="2"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
460 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
461 <param name="inputmz" value="328.9"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
462 <param name="plusminus_dalton" value="0.25"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
463 <output name="filtering_qc" file="imzml_filtered2.pdf" compare="sim_size" delta="20000"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
464 <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
465 </test>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
466 <test expect_num_outputs="3">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
467 <param name="infile" value="" ftype="imzml">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
468 <composite_data value="Example_Continuous.imzML"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
469 <composite_data value="Example_Continuous.ibd"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
470 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
471 <param name="pixel_filtering" value="pixel_range"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
472 <param name="min_x_range" value="0"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
473 <param name="max_x_range" value="10"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
474 <param name="min_y_range" value="2"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
475 <param name="max_y_range" value="2"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
476 <param name="features_filtering" value="features_range"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
477 <param name="min_mz" value="200" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
478 <param name="max_mz" value="500"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
479 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
480 <param name="inputmz" value="328.9"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
481 <param name="plusminus_dalton" value="0.25"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
482 <param name="output_matrix" value="True"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
483 <output name="filtering_qc" file="imzml_filtered3.pdf" compare="sim_size" delta="20000"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
484 <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
485 <output name="matrixasoutput" file="imzml_matrix3.tabular"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
486 </test>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
487 <test expect_num_outputs="2">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
488 <param name="infile" value="" ftype="imzml">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
489 <composite_data value="Example_Continuous.imzML"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
490 <composite_data value="Example_Continuous.ibd"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
491 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
492 <param name="pixel_filtering" value="two_columns"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
493 <param name="two_columns_pixel" ftype="tabular" value = "inputpixels_2column.tabular"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
494 <param name="pixel_column_x" value="1"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
495 <param name="pixel_column_y" value="3"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
496 <param name="features_filtering" value="features_list"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
497 <param name="inputfeatures" ftype="tabular" value = "inputcalibrantfile2.txt"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
498 <param name="feature_column" value="1"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
499 <param name="feature_header" value="0"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
500 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
501 <param name="inputmz" value="328.9"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
502 <param name="plusminus_dalton" value="0.25"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
503 <output name="filtering_qc" file="imzml_filtered4.pdf" compare="sim_size" delta="20000"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
504 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
505 </test>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
506 <test expect_num_outputs="2">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
507 <param name="infile" value="" ftype="imzml">
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
508 <composite_data value="Example_Continuous.imzML"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
509 <composite_data value="Example_Continuous.ibd"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
510 </param>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
511 <param name="pixel_filtering" value="pixel_range"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
512 <param name="min_x_range" value="0"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
513 <param name="max_x_range" value="10"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
514 <param name="min_y_range" value="2"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
515 <param name="max_y_range" value="20"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
516 <param name="features_filtering" value="features_range"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
517 <param name="min_mz" value="1" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
518 <param name="max_mz" value="150"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
519 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
520 <param name="inputmz" value="328.9"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
521 <param name="plusminus_dalton" value="0.25"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
522 <output name="filtering_qc" file="imzml_filtered5.pdf" compare="sim_size" delta="20000"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
523 <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" />
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
524 </test>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
525 <test expect_num_outputs="3">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
526 <param name="infile" value="" ftype="analyze75">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
527 <composite_data value="Analyze75.hdr"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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parents:
diff changeset
528 <composite_data value="Analyze75.img"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
529 <composite_data value="Analyze75.t2m"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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parents:
diff changeset
530 </param>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
531 <param name="pixel_filtering" value="single_column"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
532 <param name="single_pixels" ftype="tabular" value = "inputpixels2.tabular"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
533 <param name="pixel_column" value="1"/>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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534 <param name="features_filtering" value="features_list"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
535 <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
536 <param name="feature_column" value="1"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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parents:
diff changeset
537 <conditional name="outputs">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
538 <param name="outputs_select" value="quality_control"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
539 <param name="inputmz" value="702"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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540 <param name="plusminus_dalton" value="0.25"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
541 </conditional>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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542 <param name="output_matrix" value="True"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
543 <output name="filtering_qc" file="analyze_filtered.pdf" compare="sim_size" delta="20000"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
544 <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" />
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
545 <output name="matrixasoutput" file="analyze_matrix.tabular"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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546 </test>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
547 <test expect_num_outputs="2">
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
548 <param name="infile" value="" ftype="analyze75">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
549 <composite_data value="Analyze75.hdr"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
550 <composite_data value="Analyze75.img"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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parents:
diff changeset
551 <composite_data value="Analyze75.t2m"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
552 </param>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
553 <conditional name="outputs">
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
554 <param name="outputs_select" value="quality_control"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
555 <param name="inputmz" value="702"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
556 <param name="plusminus_dalton" value="0.25"/>
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
557 </conditional>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
558 <output name="filtering_qc" file="analyze75_filtered2.pdf" compare="sim_size" delta="20000"/>
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
559 <output name="msidata_filtered" file="analyze_originaloutput2.RData" compare="sim_size" />
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
560 </test>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
561 <test expect_num_outputs="2">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
562 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
563 <conditional name="outputs">
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
564 <param name="outputs_select" value="no_quality_control"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
565 </conditional>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
566 <param name="output_matrix" value="True"/>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
567 <output name="matrixasoutput" file="rdata_matrix.tabular"/>
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
568 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size" />
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
569 </test>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
570 </tests>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
571 <help>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
572 <![CDATA[
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
573
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
574 This tool can filter three types of mass-spectrometry imaging files (see below) for pixels and features of interest. This can be used to keep only pixels in a regions of interest.
1
a170455feb59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
575 For filtering at least one valid pixel/feature is needed otherwise no filtering will be performed. It is recommended to use the filtering tool only for feature masses which have been extracted from the same dataset. If you have feature masses from dataset A and you want to use them to filter dataset B, first find the corresponding (closest) features in dataset B by using the tool "Join two files on column allowing a small difference". Afterwards use the corresponding feature masses from dataset B to filter dataset B.
0
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
576
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
577 Input data: 3 types of input data can be used:
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
578
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
579 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
580 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
581 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
582
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
583 The output of this tool is a subsetted Cardinal "MSImageSet" with the variable name "msidata" saved as .RData.
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
584 ]]>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
585 </help>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
586 <citations>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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diff changeset
587 <citation type="doi">10.1093/bioinformatics/btv146</citation>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
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diff changeset
588 </citations>
91e2a0c9695c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
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589 </tool>