Mercurial > repos > galaxyp > cardinal_spectra_plots

annotate spectra_plots.xml @ 1:45fb4dd8400b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:21:18 -0400
parents de334e98f1c1
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1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1">
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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="3.0">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="1.0.0">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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30 @READING_MSIDATA@
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32 @DATA_PROPERTIES@
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35 ######################################## PDF ###################################
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36 ################################################################################
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37 ################################################################################
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40 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
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41 plot(0,type='n',axes=FALSE,ann=FALSE)
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42 #if not $filename:
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43 #set $filename = $infile.display_name
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44 #end if
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45 title(main=paste0("Mass spectra for file: \n\n","$filename"))
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48 ############################# I) numbers ######################################
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49 ###############################################################################
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51 grid.table(property_df, rows= NULL)
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53 ## set NA to 0 otherwise plot function will not work
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55 ##spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
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57 spectra_df = spectra(msidata)[]
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58 spectra_df[is.na(spectra_df)] = 0
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59 print(paste0("Number of NA which were converted into 0:",sum(is.na(spectra_df))))
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60 spectra(msidata) = spectra_df
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61
0
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63 if (npeaks > 0){
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65 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
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66
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67 ############################# single pixel ################################
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68 ###########################################################################
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70 #if str( $pixel_conditional.pixel_type) == 'single_pixel':
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71 print("single_pixel")
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73 #for $chosenpixel in $pixel_conditional.repeatpixel:
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75 pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy)
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76 pixelisvalid = as.character(pixelname %in% names(pixels(msidata)))
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77 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
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79 ############################# II) control image ####################
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81 if (pixelisvalid == "TRUE"){
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82 print(pixelisvalid)
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84 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
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85 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
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86 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
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87
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88 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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89 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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90
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91 ##################### III) plot full mass spectrum #################
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92
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93 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
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94
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95 ##################### IV) plot zoom-in mass spectrum ###############
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96
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97 #if $chosenpixel.zoomedplot:
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98
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99 #for $token in $chosenpixel.zoomedplot:
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100
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101 minmasspixel = features(msidata, mz=$token.xlimmin)
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102 maxmasspixel = features(msidata, mz=$token.xlimmax)
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103
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104 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
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105 xlim= c($token.xlimmin,$token.xlimmax))
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106
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107 #end for
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108 #end if
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109 }else{
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110 print("The pixel coordinates did not correspond to a real pixel")}
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111 #end for
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112
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113 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
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114
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115 ############################# sample pixel ################################
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116 ###########################################################################
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117
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118 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
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119 print("sample pixels")
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120
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121 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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122
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123 #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation':
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124
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125 ## read and extract x,y,annotation information
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126 input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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127 annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)]
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128 colnames(annotation_input) = c("x", "y", "annotation")
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129
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130 ## merge with coordinate information of msidata
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131 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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132 colnames(msidata_coordinates)[3] = "pixel_index"
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133 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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134 merged_annotation[is.na(merged_annotation)] = "NA"
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135 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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136 msidata\$annotation = as.factor(merged_annotation[,4])
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137
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138 #end if
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139
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140 ##################### I) Sample: plot full mass spectrum ##############
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141
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142 ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample
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143
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144 if (!is.null(levels(msidata\$annotation))){
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145 print("annotated samples")
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146
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147 ## overview plot over annotated samples
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148 number_combined = length(levels(msidata\$annotation))
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149
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150 ## the more annotation groups a file has the smaller will be the legend
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151 if (number_combined<20){
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152 legend_size = 10
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153 }else if (number_combined>20 && number_combined<40){
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154 legend_size = 9
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155 }else if (number_combined>40 && number_combined<60){
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156 legend_size = 8
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157 }else if (number_combined>60 && number_combined<100){
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158 legend_size = 7
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159 }else{
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160 legend_size = 6
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161 }
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162
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163 position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation))
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164 colnames(position_df)[3] = "sample_name"
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165
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166 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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167 geom_tile(height = 1, width=1)+
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168 coord_fixed()+
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169 ggtitle("Spatial orientation of pixel annotations")+
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170 theme_bw()+
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171 theme(plot.title = element_text(hjust = 0.5))+
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172 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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173 theme(legend.position="bottom",legend.direction="vertical")+
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174 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
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175 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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176
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177 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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178 coord_labels\$file_number = 1:length(levels(position_df\$sample_name))
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179
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180 for(file_count in 1:nrow(coord_labels))
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181 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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182 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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183
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184 print(combine_plot)
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185
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186 ## print legend only for less than 10 samples
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187 if (length(levels(msidata\$annotation)) < 10){
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188 key_legend = TRUE
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189 }else{key_legend = FALSE}
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190
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191 spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
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192 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
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193 }else{
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194 spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
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195 plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
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196
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197 ##################### II) Sample: plot zoom-in mass spectrum ##########
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198
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199 #if $pixel_conditional.zoomed_sample:
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200 iData(msidata) <- iData(msidata)[] ## getting back data on disk
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201 #for $token in $pixel_conditional.zoomed_sample:
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202 print("zoomed sample pixels")
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203
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204 minmasspixel = features(msidata, mz=$token.xlimmin)
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205 maxmasspixel = features(msidata, mz=$token.xlimmax)
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206
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207 ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot
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208 if (!is.null(levels(msidata\$annotation))){
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209 print("annotation samples")
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210 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
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211 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation,
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212 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE)
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213 }else{
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214 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
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215
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216 #end for
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217 #end if
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218
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219 if (!is.null(levels(msidata\$annotation))){
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220 pixeldf = data.frame(table(msidata\$annotation))
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221 }else{
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222 pixeldf = data.frame("$filename", ncol(msidata))}
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223 colnames(pixeldf) = c("sample name", "number of pixels")
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224
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225 #end if
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226
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227
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228 ############################# pixel table ######################################
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229 ###############################################################################
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230
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231
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232 ### overview table of pixels or samples:
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233 plot(0,type='n',axes=FALSE,ann=FALSE)
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234 title(main="Overview of chosen pixel:")
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235
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236 ### for more than 20 annotation groups print only 20 samples per page:
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237 if (is.null(levels(msidata\$annotation))){
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238 grid.table(pixeldf, rows= NULL)
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239 }else if (length(levels(msidata\$annotation)) <= 20){
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240 grid.table(pixeldf, rows= NULL)
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241 }else{
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242 grid.table(pixeldf[1:20,], rows= NULL)
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243 mincount = 21
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244 maxcount = 40
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245 for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
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246 plot(0,type='n',axes=FALSE,ann=FALSE)
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247 if (maxcount <= nrow(pixeldf)){
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248 grid.table(pixeldf[mincount:maxcount,], rows= NULL)
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249 mincount = mincount+20
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250 maxcount = maxcount+20
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251 }else{### stop last page with last sample otherwise NA in table
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252 grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
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253 }
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254 }
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255
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256 dev.off()
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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258 }else{
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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259 print("Inputfile has no intensities > 0")
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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260 dev.off()
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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261 }
1
45fb4dd8400b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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262
45fb4dd8400b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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263
0
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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264 ]]></configfile>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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265 </configfiles>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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266 <inputs>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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267 <expand macro="reading_msidata"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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268 <expand macro="pdf_filename"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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269 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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270 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or the average spectrum of all pixels of a sample">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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271 <option value="single_pixel" selected="True">Single pixel</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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272 <option value="sample_pixel">Average spectrum for each sample</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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273 </param>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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274 <when value="single_pixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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275 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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276 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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277 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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278 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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279 <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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280 <param name="inputcolour" type="select" label="Select the colour for the lines at x and y position">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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281 <option value="white" selected="True">white</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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282 <option value="black">black</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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283 <option value="grey">grey</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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284 <option value="blue">blue</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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285 <option value="red">red</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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286 <option value="green">green</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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287 </param>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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288 <param name="inputtype" type="select" label="Select the line type for the lines at x and y position">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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289 <option value="solid" selected="True">solid</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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290 <option value="dashed">dashed</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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291 <option value="dotted">dotted</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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292 <option value="longdash">longdash</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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293 </param>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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294 <param name="inputwidth" type="integer" value="2" label="Select the width of the lines at x and y position"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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295 <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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296 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
297 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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298 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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299 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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300 </when>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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301 <when value="sample_pixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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302 <conditional name="tabular_annotation">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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303 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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304 <option value="no_annotation" selected="True">pixels belong into one group only</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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305 <option value="yes_annotation">group pixels according to annotations</option>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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306 </param>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
307 <when value="yes_annotation">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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308 <expand macro="reading_pixel_annotations"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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309 </when>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
310 <when value="no_annotation"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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311 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
312 <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
313 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
314 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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315 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 </when>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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317 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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318 </inputs>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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319 <outputs>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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320 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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321 </outputs>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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322 <tests>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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323 <test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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324 <expand macro="infile_imzml"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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325 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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326 <param name="pixel_type" value="single_pixel"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
327 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
328 <param name="plusminusinDalton" value="0.25"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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329 <param name="inputx" value="3"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
330 <param name="inputy" value="3"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
331 <repeat name="zoomedplot">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
332 <param name="xlimmin" value="310"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
333 <param name="xlimmax" value="320"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
334 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
335 <repeat name="zoomedplot">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
336 <param name="xlimmin" value="350"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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337 <param name="xlimmax" value="400"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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338 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
339 <repeat name="zoomedplot">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
340 <param name="xlimmin" value="400"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
341 <param name="xlimmax" value="420"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
342 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
343 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
344 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
345 <param name="plusminusinDalton" value="0.25"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
346 <param name="inputx" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
347 <param name="inputy" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
348 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
349 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
350 <param name="plusminusinDalton" value="0.25"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
351 <param name="inputx" value="1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
352 <param name="inputy" value="1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
353 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
354 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
355 <output name="plots" file="Plot_imzml.pdf" compare="sim_size"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
356 </test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
357 <test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358 <expand macro="infile_analyze75"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
359 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
360 <param name="pixel_type" value="single_pixel"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
361 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362 <param name="plusminusinDalton" value="0.25"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
363 <param name="inputx" value="5"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
364 <param name="inputy" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 <repeat name="zoomedplot">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366 <param name="xlimmin" value="840"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
367 <param name="xlimmax" value="850"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
368 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
369 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
370 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
371 <param name="plusminusinDalton" value="0.25"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
372 <param name="inputx" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
373 <param name="inputy" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
374 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 </test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
378 <test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 <expand macro="infile_analyze75"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381 <param name="pixel_type" value="sample_pixel"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 <conditional name="tabular_annotation">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
383
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 <param name="load_annotation" value="yes_annotation"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
385 <param name="annotation_file" value="annotations.tabular" ftype="tabular"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
386 <param name="column_x" value="1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
387 <param name="column_y" value="2"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
388 <param name="column_names" value="4"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
389 <param name="tabular_header" value="TRUE"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
391
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
392
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
393 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
394 <repeat name="zoomed_sample">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395 <param name="xlimmin" value="1250"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
396 <param name="xlimmax" value="1270"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
397 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
398 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
399 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
400 </test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 <test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 <param name="pixel_type" value="sample_pixel"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
405 <repeat name="zoomed_sample">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 <param name="xlimmin" value="350"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407 <param name="xlimmax" value="360"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
408 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
409 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
410 <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
411 </test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
412 <test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414 <conditional name="pixel_conditional">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 <param name="pixel_type" value="single_pixel"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416 <repeat name="repeatpixel">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 <param name="plusminusinDalton" value="0.1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418 <param name="inputx" value="1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
419 <param name="inputy" value="1"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
420 </repeat>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421 </conditional>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 </test>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 </tests>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <help><![CDATA[
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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427 @CARDINAL_DESCRIPTION@
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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428
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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429 -----
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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430
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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431 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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432
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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433 @MSIDATA_INPUT_DESCRIPTION@
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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434 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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435
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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436 **Options**
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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437
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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438 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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439
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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440 - Enter the x and y coordinates of your pixel of interest
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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441 - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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442 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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443
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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444 - "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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445
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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446 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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447
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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448
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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449 **Tip**
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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450
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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451 - Corresponding m/z intensity pairs for single spectra can be obtained with the filtering tool option "ranges for x and y" and afterwards using the imzml tabular exporter tool
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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452 - Plots will only be drawn for pixels that exist in the MSI data, pixel that are outside the dataset will be "False" in the overview table on the last page of the pdf
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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453
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454
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455 **Output**
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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456
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457 - Pdf with the selected mass spectra plots and additional x-y grid plots
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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458
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459
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460 ]]>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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461 </help>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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462 <expand macro="citations"/>
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463 </tool>