Mercurial > repos > galaxyp > cardinal_spectra_plots

annotate spectra_plots.xml @ 16:12dde78d554b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
author galaxyp
date Tue, 22 Feb 2022 20:54:30 +0000
parents d333733dd571
children ba92b59cd529
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1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
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2 <description>
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3 mass spectrometry imaging mass spectra plots
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
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10 <requirement type="package" version="2.3">r-gridextra</requirement>
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11 <requirement type="package" version="1.1.1">r-scales</requirement>
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12 </expand>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 @INPUT_LINKING@
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16 cat '${MSI_mzplots}' &&
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17 Rscript '${MSI_mzplots}'
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18 ]]>
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19 </command>
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20 <configfiles>
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21 <configfile name="MSI_mzplots"><![CDATA[
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23 ################################# load libraries and read file #################
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25 library(Cardinal)
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26 library(gridExtra)
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27 library(ggplot2)
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28 library(scales)
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31 @READING_MSIDATA_FULLY_COMPATIBLE@
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33 @DATA_PROPERTIES@
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36 ######################################## PDF ###################################
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37 ################################################################################
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38 ################################################################################
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41 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
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42 plot(0,type='n',axes=FALSE,ann=FALSE)
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43 #if not $filename:
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44 #set $filename = $infile.display_name
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45 #end if
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46 title(main=paste0("Mass spectra for file: \n\n","$filename"))
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49 ############################# I) numbers ######################################
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50 ###############################################################################
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52 grid.table(property_df, rows= NULL)
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54 ## run only if mz and pixels are > 0
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56 if (ncol(msidata)>0 & nrow(msidata) >0){
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58 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
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60 ############################# single pixel ################################
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61 ###########################################################################
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63 #if str( $pixel_conditional.pixel_type) == 'tabular_pixel':
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64 print("tabular_pixel")
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66 ## read and extract x,y, optional annotation information
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67 spectra_tabular = read.delim("$pixel_conditional.pixel_file", header = $pixel_conditional.tabular_pixel_header, stringsAsFactors = FALSE)
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69 #if str($pixel_conditional.single_or_overlaid.plot_type) == 'overlaid_plots':
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71 spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.single_or_overlaid.column_pixel_annotation)]
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72 colnames(spectra_input) = c("x", "y", "annotation")
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73 spectra_input\$annotation = as.character(spectra_input\$annotation)
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75 ## keeping only spectra with annotations
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76 input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_")
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77 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
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78 pixelsofinterest = dataset_pixels %in% input_pixels
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79 msidata = msidata[,pixelsofinterest]
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80
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81 msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
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82 colnames(msidata_coordinates) = c("x", "y", "pixel_index")
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83 merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
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84 merged_annotation[is.na(merged_annotation)] = "NA"
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85 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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86 msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order
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87
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88 print(msidata\$annotation)
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89 print(merged_annotation)
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90
0
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91 ## overview plot over annotated samples
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92 number_combined = length(levels(msidata\$annotation))
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93
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94 ## the more annotation groups a file has the smaller will be the legend
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95 if (number_combined<20){
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96 legend_size = 10
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97 }else if (number_combined>20 && number_combined<40){
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98 legend_size = 9
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99 }else if (number_combined>40 && number_combined<60){
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100 legend_size = 8
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101 }else if (number_combined>60 && number_combined<100){
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102 legend_size = 7
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103 }else{
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104 legend_size = 6
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105 }
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106
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107 ## colours selection:
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108
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109 #if str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "manual_colour"
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110 #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $pixel_conditional.single_or_overlaid.colour_conditional.colours])
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111 colourvector = c($color_string)
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112
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113 #elif str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "colourpalette"
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114
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115 number_levels = (length(levels(msidata\$annotation)))
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116
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117 colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels)
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118
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119 #end if
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120
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121 position_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, as.factor(msidata\$annotation))
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122 colnames(position_df) = c("x", "y", "sample_name")
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123 print(position_df)
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124 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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125 geom_tile(height = 1, width=1)+
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126 coord_fixed()+
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127 ggtitle("Spatial orientation of annotations")+
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128 theme_bw()+
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129 theme(plot.title = element_text(hjust = 0.5))+
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130 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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131 theme(legend.position="bottom",legend.direction="vertical")+
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132 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 10))+
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133 guides(fill=guide_legend(ncol=4,byrow=TRUE))+
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134 scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector)
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135
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136 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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137 coord_labels\$file_number = 1:nrow(coord_labels)
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138
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139 for(file_count in 1:nrow(coord_labels))
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140 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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141 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))
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142 }
0
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143
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144 print(combine_plot)
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145
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146 ## print legend only for less than 10 samples
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147 if (length(levels(msidata\$annotation)) < 10){
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148 key_legend = TRUE
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149 }else{key_legend = FALSE}
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150
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151 #if $fullmz:
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152 ## plot single tabular mz, average per annotation
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153 print(plot(msidata, run="infile", pixel.groups=msidata\$annotation, key=key_legend,superpose=TRUE, strip=FALSE, grid=$grid_variable, col = colourvector), main="Average spectrum per group")
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154 #end if
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155
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156 pixeldf = data.frame(table(msidata\$annotation))
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157 colnames(pixeldf) = c("sample name", "number of pixels")
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158
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159 ##################### II) Sample: plot zoom-in mass spectrum ##########
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160
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161 #if str($mz_range.mz_range_options) == "manual_mz":
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162
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163 #for $token in $mz_range.zoomed_sample:
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164
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165
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166 minmasspixel = tryCatch(
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167 {
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168 features(msidata, mz=$token.xlimmin)
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169 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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170 warning=function(cond) {
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171 ## if xlimmin is outside mz range, use min mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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172 return(features(msidata, mz=min(mz(msidata))))
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173 }
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174 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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175
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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176 maxmasspixel = tryCatch(
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177 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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178 features(msidata, mz=$token.xlimmax)
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179 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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180 warning=function(cond) {
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181 ## if xlimax is outside mz range, use max mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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182 return(features(msidata, mz=max(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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183 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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184 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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185
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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186 ## plot single tabular mz, average per annotation, manual zoom
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c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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187 print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, col = colourvector,
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64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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188 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable,
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c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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189 key=key_legend, superpose=TRUE, main="Average spectrum per group"))
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190 #end for
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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191
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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192 #elif str($mz_range.mz_range_options) == "tabular_mz":
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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193
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194 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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195 input_mz_features = input_mz[,c($mz_range.column_mz)]
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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196 for (feature_count in input_mz_features){
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197
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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198 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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199
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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200 xlimmin = feature_count-$mz_range.minus_mz_tab
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201 xlimmax = feature_count+$mz_range.plus_mz_tab
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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202
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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203 minmasspixel = features(msidata, mz=xlimmin)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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204 maxmasspixel = features(msidata, mz=xlimmax)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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205
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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206 ## plot single tabular mz, average per annotation, tabular zoom
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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207 print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, main="Average spectrum per group",
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c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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208 xlim= c(xlimmin,xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, col = colourvector,
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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209 key=key_legend, superpose=TRUE))
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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210
7
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211 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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212 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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213
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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214 #end if
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c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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215 #elif str($pixel_conditional.single_or_overlaid.plot_type) == 'separate_plots':
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216
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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217
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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218 spectra_tabular = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y)]
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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219 colnames(spectra_tabular) = c("x", "y")
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220
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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221 dataset_pixels = data.frame(coord(msidata)\$x, coord(msidata)\$y)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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222 colnames(dataset_pixels) = c("x", "y")
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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223 spectra_input = merge(dataset_pixels, spectra_tabular, by=c("x", "y"))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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224 false_input = merge(spectra_tabular, spectra_input, by=c("x", "y"))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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225
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226 ## for loop for every valid spectrum (pixel)
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227 for (pixel_count in 1:nrow(spectra_input)){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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228
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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229 x_coord = spectra_input[pixel_count,1]
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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230 y_coord = spectra_input[pixel_count,2]
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231
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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232
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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233 ##################### I) Sample: plot full mass spectrum ##############
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234
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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235 #if $fullmz:
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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236 ## plot full mz for single tabular mz
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237 print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black"))
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64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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238 #end if
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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239
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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240 pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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241
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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242 input_pixels = paste(x_coord, y_coord, sep="_")
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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243 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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244 pixelisvalid = as.character(input_pixels %in% dataset_pixels)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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245
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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246 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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247
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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248
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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249 ##################### II) Sample: plot zoom-in mass spectrum ##########
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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diff changeset
250
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
251 #if str($mz_range.mz_range_options) == "manual_mz":
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
252 #for $token in $mz_range.zoomed_sample:
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
253
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
254 minmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
255 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
256 features(msidata, mz=$token.xlimmin)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
257 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
258 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
259 ## if xlimmin is outside mz range, use min mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
260 return(features(msidata, mz=min(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
261 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
262 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
263
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
264 maxmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
265 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
266 features(msidata, mz=$token.xlimmax)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
267 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
268 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
269 ## if xlimax is outside mz range, use max mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
270 return(features(msidata, mz=max(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
271 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
272 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
273
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
274 ## same min and max not possible for plot
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
275 if (minmasspixel == maxmasspixel){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
276 if (maxmasspixel == nrow(msidata)){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
277 minmasspixel = minmasspixel-1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
278 }else{
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
279 maxmasspixel = maxmasspixel+1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
280 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
281 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
282
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
283 ## print single tabular mz; manual zoom
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
284
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
285 tryCatch(
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
286 {
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
287 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
288 }
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
289 ,
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
290 error=function(cond) {
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
291 ## if there are no intensities > 0 in the chosen plotting window, write a warning
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
292 text(0.5,0.5,labels = c(paste("No peaks in the spectrum with the coordinates x =", x_coord, ", y =", y_coord, sep=" ")))
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
293 }
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
294 )
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
295
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
296 #end for
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
297
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
298 #elif str($mz_range.mz_range_options) == "tabular_mz":
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
299
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
300 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
301 input_mz_features = input_mz[,c($mz_range.column_mz)]
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
302 for (feature_count in input_mz_features){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
303
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
304 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
305
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
306 xlimmin = feature_count-$mz_range.minus_mz_tab
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
307 xlimmax = feature_count+$mz_range.plus_mz_tab
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
308
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
309 minmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
310 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
311 features(msidata, mz=xlimmin)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
312 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
313 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
314 ## if xlimmin is outside mz range, use min mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
315 return(features(msidata, mz=min(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
316 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
317 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
318
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
319 maxmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
320 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
321 maxmasspixel = features(msidata, mz=xlimmax)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
322 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
323 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
324 ## if xlimax is outside mz range, use max mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
325 return(features(msidata, mz=max(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
326 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
327 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
328
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
329 ## same min and max not possible for plot
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
330 if (minmasspixel == maxmasspixel){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
331 if (maxmasspixel == nrow(msidata)){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
332 minmasspixel = minmasspixel-1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
333 }else{
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
334 maxmasspixel = maxmasspixel+1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
335 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
336 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
337
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
338 ## print single tabular mz; tabular zoom
12
10566783d718 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 9
diff changeset
339 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black"))
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
340 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
341 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
342
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
343 #end if
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
344
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
345 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
346
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
347 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
348
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
349 #end if
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
350
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
351
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
352 ############################# all pixel ################################
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
353 ###########################################################################
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
354
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
355 #elif str( $pixel_conditional.pixel_type) == 'all_pixel':
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
356 print("all pixels")
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
357
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
358 ##################### I) Sample: plot full mass spectrum ##############
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
359
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
360 #if $fullmz:
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
361
12
10566783d718 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 9
diff changeset
362 print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black"))
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
363 #end if
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
364
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 ##################### II) Sample: plot zoom-in mass spectrum ##########
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
367 #if str($mz_range.mz_range_options) == "manual_mz":
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
368 #for $token in $mz_range.zoomed_sample:
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
369
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
370 minmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
371 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
372 features(msidata, mz=$token.xlimmin)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
373 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
374 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
375 ## if xlimmin is outside mz range, use min mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
376 return(features(msidata, mz=min(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
377 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
378 )
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
380 maxmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
381 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
382 features(msidata, mz=$token.xlimmax)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
383 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
384 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
385 ## if xlimax is outside mz range, use max mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
386 return(features(msidata, mz=max(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
387 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
388 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
389
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
390 ## same min and max not possible for plot
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
391 if (minmasspixel == maxmasspixel){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
392 if (maxmasspixel == nrow(msidata)){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
393 minmasspixel = minmasspixel-1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
394 }else{
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
395 maxmasspixel = maxmasspixel+1
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
396 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
397 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
398
12
10566783d718 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 9
diff changeset
399 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
400
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 #end for
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
402
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
403 #elif str($mz_range.mz_range_options) == "tabular_mz":
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
404
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
405 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
406 input_mz_features = input_mz[,c($mz_range.column_mz)]
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
407 for (feature_count in input_mz_features){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
408
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
409 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
410
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
411 xlimmin = feature_count-$mz_range.minus_mz_tab
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
412 xlimmax = feature_count+$mz_range.plus_mz_tab
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
413
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
414 minmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
415 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
416 features(msidata, mz=xlimmin)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
417 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
418 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
419 ## if xlimmin is outside mz range, use min mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
420 return(features(msidata, mz=min(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
421 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
422 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
423
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
424 maxmasspixel = tryCatch(
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
425 {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
426 maxmasspixel = features(msidata, mz=xlimmax)
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
427 },
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
428 warning=function(cond) {
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
429 ## if xlimax is outside mz range, use max mz value
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
430 return(features(msidata, mz=max(mz(msidata))))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
431 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
432 )
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
433
12
10566783d718 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 9
diff changeset
434 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black"))
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
435 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
436 }
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
437
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
438
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 #end if
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
441 pixeldf = data.frame("$filename", ncol(msidata))
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
442 colnames(pixeldf) = c("sample name", "number of pixels")
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 #end if
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
445
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
447 ############################# pixel table ######################################
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
448 ###############################################################################
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 ### overview table of pixels or samples:
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 plot(0,type='n',axes=FALSE,ann=FALSE)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 title(main="Overview of chosen pixel:")
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 ### for more than 20 annotation groups print only 20 samples per page:
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 if (is.null(levels(msidata\$annotation))){
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457 grid.table(pixeldf, rows= NULL)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 }else if (length(levels(msidata\$annotation)) <= 20){
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 grid.table(pixeldf, rows= NULL)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 }else{
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 grid.table(pixeldf[1:20,], rows= NULL)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 mincount = 21
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 maxcount = 40
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 plot(0,type='n',axes=FALSE,ann=FALSE)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 if (maxcount <= nrow(pixeldf)){
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 grid.table(pixeldf[mincount:maxcount,], rows= NULL)
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 mincount = mincount+20
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 maxcount = maxcount+20
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 }else{### stop last page with last sample otherwise NA in table
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 }
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 }
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 dev.off()
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 }else{
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 print("Inputfile has no intensities > 0")
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 dev.off()
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 }
1
1d9931768896 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
481
1d9931768896 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
482
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 ]]></configfile>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 </configfiles>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <inputs>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <expand macro="reading_msidata"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 <expand macro="pdf_filename"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 <conditional name="pixel_conditional">
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
489 <param name="pixel_type" type="select" label="Choose spectra">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
490 <option value="all_pixel" selected="True" >Plot mean spectra based on all spectra</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
491 <option value="tabular_pixel">Plot single spectra (separate or overlaid)</option>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 </param>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
493 <when value="tabular_pixel">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
494 <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
495 help="Two or three columns: x values, y values, optionally annotations"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
496 <param name="column_pixel_x" data_ref="pixel_file" label="Column with x values" type="data_column"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
497 <param name="column_pixel_y" data_ref="pixel_file" label="Column with y values" type="data_column"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
498 <param name="tabular_pixel_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
499 <conditional name="single_or_overlaid">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
500 <param name="plot_type" type="select" label="Separate plot per spectrum or overlaid plot with average spectra per annotation group">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
501 <option value="separate_plots" selected="True" >Separate spectra plots</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
502 <option value="overlaid_plots">Overlaid spectra plots</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
503 </param>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
504 <when value="separate_plots"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
505 <when value="overlaid_plots">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
506 <param name="column_pixel_annotation" data_ref="pixel_file" label="Select column with annotations" type="data_column"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
507 <conditional name="colour_conditional">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
508 <param name="colour_type" type="select" label="Choose a colour scheme">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
509 <option value="colourpalette" selected="True" >Colour palette</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
510 <option value="manual_colour">Manual selection</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
511 </param>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
512 <when value="manual_colour">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
513 <repeat name="colours" title="Colours for the plots" min="1" max="50">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
514 <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
515 <sanitizer>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
516 <valid initial="string.letters,string.digits">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
517 <add value="#" />
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
518 </valid>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
519 </sanitizer>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
520 </param>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
521 </repeat>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
522 </when>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
523 <when value="colourpalette">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
524 <param name="palettes" type="select" display="radio" label="Select a colourpalette">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
525 <option value="hue_pal()" selected="True">hue</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
526 <option value="rainbow">rainbow</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
527 <option value="heat.colors">heat colors</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
528 <option value="terrain.colors">terrain colors</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
529 <option value="topo.colors">topo colors</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
530 <option value="cm.colors">cm colors</option>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
531 </param>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
532 </when>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
533 </conditional>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
534 </when>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
535 </conditional>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
536 </when>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
537 <when value="all_pixel">
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 </when>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
539 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
540 <param name="fullmz" type="boolean" label="Plot complete m/z range" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
541 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
542 <param name="mz_range_options" type="select" label="zoomed in m/z range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
543 <option value="none_mz" selected="True">no m/z range</option>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
544 <option value="manual_mz" >Manual input</option>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
545 <option value="tabular_mz">Tabular file</option>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
546 </param>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
547 <when value="none_mz"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
548 <when value="tabular_mz">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
549 <param name="minus_mz_tab" type="float" value="" label="m/z value to subtract from m/z values in tabular file = lower m/z boundary"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
550 <param name="plus_mz_tab" type="float" value="" label="m/z value to add to m/z values in tabular file = upper m/z boundary"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
551 <param name="mz_file" type="data" format="tabular" label="Load tabular file with m/z values"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
552 <param name="column_mz" data_ref="mz_file" label="Column with mz values" type="data_column"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
553 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
554 </when>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
555 <when value="manual_mz">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
556 <repeat name="zoomed_sample" title="Define min m/z and max m/z for the plotting window" min="1">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
557 <param name="xlimmin" type="float" value="" label="lower m/z boundary for plotting window"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
558 <param name="xlimmax" type="float" value="" label="upper m/z boundary for plotting window"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 </repeat>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560 </when>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 </conditional>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
562 <param name="grid_variable" type="boolean" label="Add grid to plot" truevalue="TRUE" falsevalue="FALSE"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563 </inputs>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564 <outputs>
2
3642ed221eb2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
565 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}:results"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 </outputs>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 <tests>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
568 <test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 <expand macro="infile_imzml"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 <conditional name="pixel_conditional">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
571 <param name="pixel_type" value="tabular_pixel"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
572 <param name="pixel_file" value="spectra_1_pixel.tabular"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
573 <param name="column_pixel_x" value="1"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
574 <param name="column_pixel_y" value="2"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
575 <param name="tabular_pixel_header" value="FALSE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
576 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
577 <param name="fullmz" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
578 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
579 <param name="mz_range_options" value="manual_mz"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
580 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
581 <param name="xlimmin" value="310"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
582 <param name="xlimmax" value="320"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
583 </repeat>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
584 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
585 <param name="xlimmin" value="350"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
586 <param name="xlimmax" value="400"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
587 </repeat>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
588 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
589 <param name="xlimmin" value="360"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
590 <param name="xlimmax" value="360.8"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
591 </repeat>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592 </conditional>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
593 <param name="grid_variable" value="TRUE"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594 <output name="plots" file="Plot_imzml.pdf" compare="sim_size"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595 </test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 <test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 <expand macro="infile_analyze75"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598 <conditional name="pixel_conditional">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
599 <param name="pixel_type" value="tabular_pixel"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
600 <param name="pixel_file" value="spectra_1_pixel.tabular"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
601 <param name="column_pixel_x" value="1"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
602 <param name="column_pixel_y" value="2"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
603 <param name="tabular_pixel_header" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
604 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
605 <param name="fullmz" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
606 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
607 <param name="mz_range_options" value="manual_mz"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
608 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
609 <param name="xlimmin" value="840"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
610 <param name="xlimmax" value="850"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
611 </repeat>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
612 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
613 <param name="grid_variable" value="FALSE"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
614 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
615 </test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
616 <test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
617 <expand macro="infile_analyze75"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
618 <conditional name="pixel_conditional">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
619 <param name="pixel_type" value="tabular_pixel"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
620 <param name="pixel_file" value="annotations.tabular"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
621 <param name="column_pixel_x" value="1"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
622 <param name="column_pixel_y" value="2"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
623 <param name="tabular_pixel_header" value="TRUE"/>
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
624
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
625 <conditional name="single_or_overlaid">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
626 <param name="plot_type" value="overlaid_plots"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
627 <param name="column_pixel_annotation" value="4"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
628 <param name="colour_type" value="manual_colour"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
629 <repeat name="colours">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
630 <param name="annotation_color" value="#0000FF"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
631 </repeat>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
632 <repeat name="colours">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
633 <param name="annotation_color" value="#00C957"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
634 </repeat>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
635 <repeat name="colours">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
636 <param name="annotation_color" value="#B0171F"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
637 </repeat>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
638 </conditional>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
639 </conditional>
13
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
640 <param name="fullmz" value="FALSE"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
641 <conditional name="mz_range">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
642 <param name="mz_range_options" value="manual_mz"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
643 <repeat name="zoomed_sample">
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
644 <param name="xlimmin" value="1250"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
645 <param name="xlimmax" value="1270"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
646 </repeat>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
647 </conditional>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
648 <param name="grid_variable" value="FALSE"/>
c5aa9fca18c6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
649 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
650 </test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
651 <test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
652 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
653 <conditional name="pixel_conditional">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
654 <param name="pixel_type" value="all_pixel"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
655 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
656 <param name="fullmz" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
657 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
658 <param name="mz_range_options" value="manual_mz"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
659 <repeat name="zoomed_sample">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
660 <param name="xlimmin" value="350"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
661 <param name="xlimmax" value="360"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
662 </repeat>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
663 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
664 <param name="grid_variable" value="FALSE"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
665 <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
666 </test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
667 <test>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
668 <expand macro="processed_infile_imzml"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
669 <conditional name="processed_cond">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
670 <param name="processed_file" value="processed"/>
9
0b7e00e5b9d2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
671 <param name="accuracy" value="100"/>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
672 <param name="units" value="ppm"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
673 </conditional>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
674 <conditional name="pixel_conditional">
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
675 <param name="pixel_type" value="all_pixel"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
676 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
677 <param name="fullmz" value="FALSE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
678 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
679 <param name="mz_range_options" value="manual_mz"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
680 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
681 <param name="xlimmin" value="350"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
682 <param name="xlimmax" value="350.5"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
683 </repeat>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
684 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
685 <param name="xlimmin" value="600"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
686 <param name="xlimmax" value="650"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
687 </repeat>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
688 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
689 <param name="grid_variable" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
690 <output name="plots" file="Plot_processed.pdf" compare="sim_size"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
691 </test>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
692 <test>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
693 <param name="infile" value="" ftype="imzml">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
694 <composite_data value="preprocessing_results1.imzml"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
695 <composite_data value="preprocessing_results1.ibd"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
696 </param>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
697 <param name="centroids" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
698 <conditional name="pixel_conditional">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
699 <param name="pixel_type" value="all_pixel"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
700 </conditional>
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
701 <param name="fullmz" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
702 <conditional name="mz_range">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
703 <param name="mz_range_options" value="manual_mz"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
704 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
705 <param name="xlimmin" value="328"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
706 <param name="xlimmax" value="330"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
707 </repeat>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
708 <repeat name="zoomed_sample">
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
709 <param name="xlimmin" value="335"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
710 <param name="xlimmax" value="340"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
711 </repeat>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
712 </conditional>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
713 <param name="grid_variable" value="TRUE"/>
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
714 <output name="plots" file="Plot_picked.pdf" compare="sim_size"/>
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
715 </test>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
716 </tests>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
717 <help><![CDATA[
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
718
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
719 @CARDINAL_DESCRIPTION@
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
720
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721 -----
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
722
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
723 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
724
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
725 @MSIDATA_INPUT_DESCRIPTION@
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
726
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
727 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
728
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
729 @MZ_TABULAR_INPUT_DESCRIPTION@
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
730
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
731 **Options**
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
732
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
733 *Choosing spectra*
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
734
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
735 - "All spectra": Plots average mass spectra (mean of all spectra)
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
736
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
737 - "Single spectra": Returns a full mass spectrum plot for each input spectrum, which is defined by its x- and y-coordinates
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
738
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
739 - the annotation column is optional:
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
740 - without annotation column: plots a separate mass spectrum for every input spectrum
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
741 - with annotation column: plots average mass spectra for each annotation group in different colours
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
742
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
743
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
744 *Choosing m/z axis*
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
745
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
746 - "Plot complete m/z range": Full m/z range is plotted
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
747
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
748 - "zoomed in m/z range": Only a customized m/z range is plotted
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
749
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
750
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
751 - "Manual input": Provide the minimum and maximum m/z value to define the m/z axis of the plot
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
752
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
753 - "Tabular input": File with m/z values of interest. Needs manual choice of m/z values to subtract and add from the input m/z values to generate the m/z axis of the plot
0
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
754
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
755
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
756 **Output**
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
757
7
64ea4507e0bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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758 - Single Pdf with all mass spectra plots
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9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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759
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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760
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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761 ]]>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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762 </help>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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763 <expand macro="citations"/>
9c03e7a617cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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764 </tool>