Mercurial > repos > galaxyp > cardinal_mz_images

annotate mz_images.xml @ 18:ae304a72db7b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author galaxyp
date Thu, 04 Jul 2024 13:42:18 +0000
parents 5629069fca8f
children
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1 <tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description>
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3 mass spectrometry imaging m/z heatmaps
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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 <command detect_errors="aggressive">
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10 <![CDATA[
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11 @INPUT_LINKING@
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12 cat '${MSI_heatmaps}' &&
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13 Rscript '${MSI_heatmaps}'
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <configfile name="MSI_heatmaps"><![CDATA[
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19 ################################# load libraries and read file #################
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21 library(Cardinal)
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22 library(gridExtra)
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23 ##library(lattice)
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25 @READING_MSIDATA_FULLY_COMPATIBLE@
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27 @DATA_PROPERTIES@
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29 ##in case it exists, remove z-dimension:
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30 coord(msidata)\$z <- NULL
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32 ##################################### read and filter input m/z ##############
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34 input_list = read.delim("$calibrant_file", header = $calibrant_header, stringsAsFactors = FALSE)
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35 input_list = input_list[,c($mz_column, $name_column)]
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37 ### calculate how many input m/z are valid:
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38 inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
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39 inputmz = as.numeric(inputmasses[,1])
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40 inputnames = as.character(inputmasses[,2])
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43 ############################## PDF #############################################
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44 ################################################################################
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46 pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)
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47 plot(0,type='n',axes=FALSE,ann=FALSE)
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48 #if not $filename:
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49 #set $filename = $infile.display_name
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50 #end if
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51 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))
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53 new_row = data.frame(paste0("# valid m/z in \n", "$calibrant_file.display_name"), paste0(length(inputmz), "/", length(input_list[,1])))
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54 colnames(new_row) = c("properties", "values")
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55 property_df = rbind(property_df, new_row)
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57 grid.table(property_df, rows= NULL)
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59 ############################# II) images ####################################
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61 ### only plot images when file has features and pixels:
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62 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
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64 #if str($light_mode) == "white":
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65 lightmode()
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66 #else
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67 darkmode()
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68 #end if
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69
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70 if (ncol(msidata)>0 & nrow(msidata) >0){
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71 if (length(inputmz) != 0){
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72 for (mass in 1:length(inputmz)){
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73
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74 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast",
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75 smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy)))
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76 title(inputnames[mass], adj = 0.5, line = 1)}
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79 ## optional svg output with original coordinates
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80 #if $svg_pixelimage:
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81 print("svg pixel image")
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82 ## reverse y axis for svg output = correct order and nice svg image
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83 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
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84
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
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85 msidata = as(msidata,"MSImagingExperiment")
7
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parents: 3
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86
3
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87 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
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88 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
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89 #if str($light_mode) == "white":
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90 lightmode()
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91 #else
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92 darkmode()
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93 #end if
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94 print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", alpha.power=$alpha_power, normalize.image="$normalize_image"))
0
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95 dev.off()
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96 #end if
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97
2
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98 ## optional overlay all input m/z in one image
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99 #if str($overlay_cond.overlay_selection) == "yes_overlay":
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100
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101 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
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102 colourvector = c($color_string)
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103 print(image(msidata, mz=inputmz,
2
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104 plusminus = $plusminus_dalton,
13
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105 col=colourvector,
2
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106 contrast.enhance = "$image_contrast",
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107 normalize.image="$normalize_image",
2
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108 smooth.image = "$image_smoothing",
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109 superpose=TRUE, main="overlay of all m/z",
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110 key=FALSE, alpha.power=$alpha_power,
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111 ylim= c(maximumy,minimumy)))
2
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112
7
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113 legend("$overlay_cond.legend_position",
2
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114 fill=colourvector,
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115 legend=as.numeric(inputmz))
2
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116 #end if
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117
0
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118 } else {print("The input m/z were invalid")}
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119 dev.off()
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120 }else{
2
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121 print("input file has no features or pixels left")
0
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122 dev.off()
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123 }
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124
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125
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126 ]]></configfile>
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127 </configfiles>
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128 <inputs>
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129 <expand macro="reading_msidata"/>
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130 <expand macro="pdf_filename"/>
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131 <expand macro="reading_2_column_mz_tabular"/>
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132
18
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133 <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/z" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/>
3
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134 <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
0
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135 <option value="none" selected="True">none</option>
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136 <option value="suppression">suppression</option>
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137 <option value="histogram">histogram</option>
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138 </param>
3
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139 <param name="image_smoothing" type="select" label="Image smoothing" help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges">
0
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140 <option value="none" selected="True">none</option>
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141 <option value="gaussian">gaussian</option>
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142 <option value="adaptive">adaptive</option>
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143 </param>
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144 <param name="colorscale" type="select" display="radio" label="Colorscale">
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145 <option value="viridis" selected="True">viridis</option>
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146 <option value="magma">magma</option>
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147 <option value="plasma">plasma</option>
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148 <option value="inferno">inferno</option>
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149 </param>
13
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150 <param name="light_mode" type="select" display="radio" label="Image Background">
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151 <option value="white" selected="True">white</option>
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152 <option value="black">black</option>
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153 </param>
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154 <param name="alpha_power" type="float" value="1" label="Alpha power" help="Opacity scaling factor (1 is linear)"/>
0
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155 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
7
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156 <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
0
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157 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
2
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158 <conditional name="overlay_cond">
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159 <param name="overlay_selection" type="select" label="Overlay image">
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160 <option value="no_overlay" selected="True">no</option>
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161 <option value="yes_overlay">yes</option>
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162 </param>
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163 <when value="no_overlay"/>
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164 <when value="yes_overlay">
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165 <repeat name="colours" title="Colours for the plots" min="1" max="50">
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166 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of m/z in tabular file">
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diff changeset
167 <sanitizer>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
168 <valid initial="string.letters,string.digits">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
169 <add value="#" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
170 </valid>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
171 </sanitizer>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
172 </param>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
173 </repeat>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
174 <param name="legend_position" type="select" display="radio" label="Position of legend">
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
175 <option value="topright" selected="True">topright</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
176 <option value="top">top</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
177 <option value="topleft">topleft</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
178 <option value="left">left</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
179 <option value="bottomleft">bottomleft</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
180 <option value="bottom">bottom</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
181 <option value="bottomright">bottomright</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
182 <option value="right">right</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
183 </param>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
184 </when>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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185 </conditional>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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186 </inputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
187 <outputs>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
188 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
189 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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190 <filter>svg_pixelimage</filter>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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191 </data>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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192 </outputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
193 <tests>
18
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 15
diff changeset
194 <test expect_num_outputs="1">
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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195 <expand macro="infile_imzml"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
196 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
197 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
198 <param name="name_column" value="2"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
199 <param name="plusminus_dalton" value="0.25"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
200 <param name="filename" value="Testfile_imzml"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
201 <param name="image_contrast" value="histogram"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
202 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
203 <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
204 </test>
18
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 15
diff changeset
205 <test expect_num_outputs="2">
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
206 <expand macro="infile_analyze75"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
207 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
208 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
209 <param name="name_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
210 <param name="plusminus_dalton" value="0.5"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
211 <param name="filename" value="Testfile_analyze75"/>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
212 <param name="colorscale" value="magma"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
213 <param name="image_smoothing" value="gaussian"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
214 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
215 <param name="svg_pixelimage" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
216 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
217 <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
218 </test>
18
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 15
diff changeset
219 <test expect_num_outputs="1">
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
220 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
221 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
222 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
223 <param name="name_column" value="2"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
224 <param name="plusminus_dalton" value="0.5"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
225 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
226 <param name="filename" value="Testfile_rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
227 <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
228 </test>
18
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 15
diff changeset
229 <test expect_num_outputs="1">
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
230 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
231 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
232 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
233 <param name="name_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
234 <param name="plusminus_dalton" value="0.5"/>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
235 <param name="colorscale" value="plasma"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
236 <param name="colorkey" value="False"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
237 <param name="filename" value="Testfile_rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
238 <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
239 </test>
18
ae304a72db7b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 15
diff changeset
240 <test expect_num_outputs="1">
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
241 <expand macro="processed_infile_imzml"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
242 <conditional name="processed_cond">
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
243 <param name="processed_file" value="processed"/>
9
08ebd8da780c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
galaxyp
parents: 7
diff changeset
244 <param name="accuracy" value="200"/>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
245 <param name="units" value="ppm"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
246 </conditional>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
247 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
248 <param name="mz_column" value="1"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
249 <param name="name_column" value="2"/>
13
a2b57ea6666e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
galaxyp
parents: 12
diff changeset
250 <param name="light_mode" value="black"/>
7
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251 <conditional name="overlay_cond">
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252 <param name="overlay_selection" value="yes_overlay"/>
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253 <repeat name="colours">
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254 <param name="feature_color" value="#ff00ff"/>
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255 </repeat>
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256 <repeat name="colours">
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257 <param name="feature_color" value="#1f497d"/>
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258 </repeat>
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259 <repeat name="colours">
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260 <param name="feature_color" value="#00b050"/>
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261 </repeat>
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262 <param name="legend_position" value="topleft"/>
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263 </conditional>
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264 <output name="plots" file="Heatmaps_processed.pdf" ftype="pdf" compare="sim_size"/>
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265 </test>
0
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266 </tests>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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267 <help><![CDATA[
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268
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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269 @CARDINAL_DESCRIPTION@
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270
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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271 -----
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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272
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273 This tool uses the Cardinal image function to plot the intensity distribution of m/z features of mass spectrometry imaging data.
0
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274
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275 @MSIDATA_INPUT_DESCRIPTION@
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276
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277 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
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278
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279
0
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280 **Tips**
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281
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282 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))
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283 - The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra
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284
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285 **Output**
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286
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287 - Single Pdf with the heatmap images
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288 - optional: svg file with the heatmap of the first valid m/z in the tabular file
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289
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290
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291 ]]>
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292 </help>
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293 <expand macro="citations"/>
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294 </tool>