Mercurial > repos > galaxyp > cardinal_mz_images

comparison mz_images.xml @ 13:a2b57ea6666e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
author galaxyp
date Sun, 29 Nov 2020 23:23:01 +0000
parents a95a82eb4d50
children 5629069fca8f
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12:a95a82eb4d50 13:a2b57ea6666e
1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1"> 1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2">
2 <description> 2 <description>
3 mass spectrometry imaging m/z heatmaps 3 mass spectrometry imaging m/z heatmaps
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
60 60
61 ############################# II) images #################################### 61 ############################# II) images ####################################
62 62
63 ### only plot images when file has features and pixels: 63 ### only plot images when file has features and pixels:
64 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend 64 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
65
66 #if str($light_mode) == "white":
67 lightmode()
68 #else
69 darkmode()
70 #end if
71
65 if (ncol(msidata)>0 & nrow(msidata) >0){ 72 if (ncol(msidata)>0 & nrow(msidata) >0){
66 if (length(inputmz) != 0){ 73 if (length(inputmz) != 0){
67 for (mass in 1:length(inputmz)){ 74 for (mass in 1:length(inputmz)){
68 75
69 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 76 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast",
70 smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy))) 77 smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy)))
71 title(inputnames[mass], adj = 0.5, line = 1)} 78 title(inputnames[mass], adj = 0.5, line = 1)}
72 79
73 80
74 ## optional svg output with original coordinates 81 ## optional svg output with original coordinates
75 #if $svg_pixelimage: 82 #if $svg_pixelimage:
79 ## works only with MSImageSet as expected 86 ## works only with MSImageSet as expected
80 msidata = as(msidata, "MSImageSet") 87 msidata = as(msidata, "MSImageSet")
81 88
82 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) 89 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
83 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg 90 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
84 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", normalize.image="$normalize_image")) 91 #if str($light_mode) == "white":
92 lightmode()
93 #else
94 darkmode()
95 #end if
96 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"))
85 dev.off() 97 dev.off()
86 #end if 98 #end if
87 99
88 ## optional overlay all input m/z in one image 100 ## optional overlay all input m/z in one image
89 #if str($overlay_cond.overlay_selection) == "yes_overlay": 101 #if str($overlay_cond.overlay_selection) == "yes_overlay":
90 102
91 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours]) 103 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
92 colourvector = c($color_string) 104 colourvector = c($color_string)
93 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
94 print(image(msidata, mz=inputmz, 105 print(image(msidata, mz=inputmz,
95 plusminus = $plusminus_dalton, 106 plusminus = $plusminus_dalton,
96 col=colourvector, 107 col=colourvector,
97 contrast.enhance = "$image_contrast", 108 contrast.enhance = "$image_contrast",
98 normalize.image="$normalize_image", 109 normalize.image="$normalize_image",
99 smooth.image = "$image_smoothing", 110 smooth.image = "$image_smoothing",
100 superpose=TRUE, main="overlay of all m/z", 111 superpose=TRUE, main="overlay of all m/z",
101 key=FALSE, 112 key=FALSE, alpha.power=$alpha_power,
102 ylim= c(maximumy,minimumy))) 113 ylim= c(maximumy,minimumy)))
103 114
104 legend("$overlay_cond.legend_position", 115 legend("$overlay_cond.legend_position",
105 fill=colourvector, 116 fill=colourvector,
106 legend=as.numeric(inputmz)) 117 legend=as.numeric(inputmz))
119 <inputs> 130 <inputs>
120 <expand macro="reading_msidata"/> 131 <expand macro="reading_msidata"/>
121 <expand macro="pdf_filename"/> 132 <expand macro="pdf_filename"/>
122 <expand macro="reading_2_column_mz_tabular"/> 133 <expand macro="reading_2_column_mz_tabular"/>
123 134
124 <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/> 135 <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" 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"/>
125 <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"> 136 <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">
126 <option value="none" selected="True">none</option> 137 <option value="none" selected="True">none</option>
127 <option value="suppression">suppression</option> 138 <option value="suppression">suppression</option>
128 <option value="histogram">histogram</option> 139 <option value="histogram">histogram</option>
129 </param> 140 </param>
136 <option value="viridis" selected="True">viridis</option> 147 <option value="viridis" selected="True">viridis</option>
137 <option value="magma">magma</option> 148 <option value="magma">magma</option>
138 <option value="plasma">plasma</option> 149 <option value="plasma">plasma</option>
139 <option value="inferno">inferno</option> 150 <option value="inferno">inferno</option>
140 </param> 151 </param>
152 <param name="light_mode" type="select" display="radio" label="Image Background">
153 <option value="white" selected="True">white</option>
154 <option value="black">black</option>
155 </param>
156 <param name="alpha_power" type="float" value="1" label="Alpha power" help="Opacity scaling factor (1 is linear)"/>
141 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> 157 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
142 <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/> 158 <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
143 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/> 159 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
144 <conditional name="overlay_cond"> 160 <conditional name="overlay_cond">
145 <param name="overlay_selection" type="select" label="Overlay image"> 161 <param name="overlay_selection" type="select" label="Overlay image">
231 <param name="units" value="ppm"/> 247 <param name="units" value="ppm"/>
232 </conditional> 248 </conditional>
233 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> 249 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
234 <param name="mz_column" value="1"/> 250 <param name="mz_column" value="1"/>
235 <param name="name_column" value="2"/> 251 <param name="name_column" value="2"/>
252 <param name="light_mode" value="black"/>
236 <conditional name="overlay_cond"> 253 <conditional name="overlay_cond">
237 <param name="overlay_selection" value="yes_overlay"/> 254 <param name="overlay_selection" value="yes_overlay"/>
238 <repeat name="colours"> 255 <repeat name="colours">
239 <param name="feature_color" value="#ff00ff"/> 256 <param name="feature_color" value="#ff00ff"/>
240 </repeat> 257 </repeat>