Mercurial > repos > galaxyp > cardinal_mz_images

annotate mz_images.xml @ 7:5e6f8fb2df07 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 08:08:28 -0400
parents 773a24b240e1
children 08ebd8da780c
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5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0">
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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 <requirement type="package" version="2.3">r-gridextra</requirement>
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10 </expand>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
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13 @INPUT_LINKING@
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14 cat '${MSI_heatmaps}' &&
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15 Rscript '${MSI_heatmaps}'
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="MSI_heatmaps"><![CDATA[
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21 ################################# load libraries and read file #################
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23 library(Cardinal)
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24 library(gridExtra)
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25 ##library(lattice)
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27 @READING_MSIDATA_FULLY_COMPATIBLE@
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29 @DATA_PROPERTIES@
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31 ##################################### read and filter input m/z ##############
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33 input_list = read.delim("$calibrant_file", header = $calibrant_header, stringsAsFactors = FALSE)
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34 input_list = input_list[,c($mz_column, $name_column)]
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36 ### calculate how many input m/z are valid:
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37 inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
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38 inputmz = as.numeric(inputmasses[,1])
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39 inputnames = as.character(inputmasses[,2])
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42 ############################## PDF #############################################
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43 ################################################################################
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45 pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)
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46 plot(0,type='n',axes=FALSE,ann=FALSE)
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47 #if not $filename:
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48 #set $filename = $infile.display_name
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49 #end if
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50 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))
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51
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52 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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53 colnames(new_row) = c("properties", "values")
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54 property_df = rbind(property_df, new_row)
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56 grid.table(property_df, rows= NULL)
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58 ############################# II) images ####################################
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59
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60 ### only plot images when file has features and pixels:
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61 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
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62 if (ncol(msidata)>0 & nrow(msidata) >0){
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63 if (length(inputmz) != 0){
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64 for (mass in 1:length(inputmz)){
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65
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66 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast",
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67 smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))}
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70 ## optional svg output with original coordinates
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71 #if $svg_pixelimage:
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72 print("svg pixel image")
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73 ## reverse y axis for svg output = correct order and nice svg image
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74 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
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75 ## works only with MSImageSet as expected
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76 msidata = as(msidata, "MSImageSet")
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77
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78 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
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79 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
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80 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="$normalize_image"))
0
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81 dev.off()
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82 #end if
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83
2
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84 ## optional overlay all input m/z in one image
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galaxyp
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85 #if str($overlay_cond.overlay_selection) == "yes_overlay":
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86
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87 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
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88 colourvector = c($color_string)
7
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89 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
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90 print(image(msidata, mz=inputmz,
2
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galaxyp
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91 plusminus = $plusminus_dalton,
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galaxyp
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92 col=colourvector,
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93 contrast.enhance = "$image_contrast",
7
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94 normalize.image="$normalize_image",
2
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galaxyp
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95 smooth.image = "$image_smoothing",
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96 superpose=TRUE, main="overlay of all m/z",
7
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97 key=FALSE,
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98 ylim= c(maximumy,minimumy)))
2
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99
7
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100 legend("$overlay_cond.legend_position",
2
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101 fill=colourvector,
7
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102 legend=as.numeric(sort(as.character(inputmz))))
2
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galaxyp
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103 #end if
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104
0
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105 } else {print("The input m/z were invalid")}
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106 dev.off()
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galaxyp
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107 }else{
2
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108 print("input file has no features or pixels left")
0
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109 dev.off()
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110 }
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111
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112
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113 ]]></configfile>
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114 </configfiles>
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115 <inputs>
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116 <expand macro="reading_msidata"/>
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117 <expand macro="pdf_filename"/>
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118 <expand macro="reading_2_column_mz_tabular"/>
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119
7
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120 <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/>
3
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121 <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
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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122 <option value="none" selected="True">none</option>
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123 <option value="suppression">suppression</option>
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124 <option value="histogram">histogram</option>
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galaxyp
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125 </param>
3
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126 <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
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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127 <option value="none" selected="True">none</option>
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128 <option value="gaussian">gaussian</option>
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129 <option value="adaptive">adaptive</option>
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130 </param>
7
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131 <param name="colorscale" type="select" display="radio" label="Colorscale">
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132 <option value="viridis" selected="True">viridis</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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133 <option value="magma">magma</option>
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134 <option value="plasma">plasma</option>
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135 <option value="inferno">inferno</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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136 </param>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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137 <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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138 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
7
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galaxyp
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139 <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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140 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
2
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galaxyp
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141 <conditional name="overlay_cond">
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galaxyp
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142 <param name="overlay_selection" type="select" label="Overlay image">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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143 <option value="no_overlay" selected="True">no</option>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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144 <option value="yes_overlay">yes</option>
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galaxyp
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145 </param>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
146 <when value="no_overlay"/>
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galaxyp
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147 <when value="yes_overlay">
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galaxyp
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148 <repeat name="colours" title="Colours for the plots" min="1" max="50">
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149 <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">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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150 <sanitizer>
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galaxyp
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151 <valid initial="string.letters,string.digits">
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galaxyp
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diff changeset
152 <add value="#" />
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galaxyp
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153 </valid>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
154 </sanitizer>
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galaxyp
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155 </param>
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156 </repeat>
7
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157 <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"
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158 <option value="topright" selected="True">topright</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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159 <option value="top">top</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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160 <option value="topleft">topleft</option>
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161 <option value="left">left</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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162 <option value="bottomleft">bottomleft</option>
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163 <option value="bottom">bottom</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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164 <option value="bottomright">bottomright</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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165 <option value="right">right</option>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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166 </param>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
167 </when>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
168 </conditional>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
169 </inputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
170 <outputs>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
171 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
172 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${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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173 <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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174 </data>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
175 </outputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
176 <tests>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
177 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
186 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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187 <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
parents:
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188 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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189 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
190 <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
191 <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
192 <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
193 <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
194 <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:
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195 <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
196 <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
197 <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
198 <param name="strip" value="False"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
199 <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
200 <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
201 <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
202 <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
203 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
204 <test>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
205 <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
206 <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
207 <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
208 <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
209 <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
210 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
211 <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
212 <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
213 <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
214 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
215 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
216 <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
217 <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
218 <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
219 <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
220 <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
221 <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
222 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
223 <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
224 <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
225 <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
226 </test>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
227 <test>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
228 <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
229 <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
230 <param name="processed_file" value="processed"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
231 <param name="accuracy" value="100"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
232 <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
233 </conditional>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
234 <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
235 <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
236 <param name="name_column" value="2"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
237 <conditional name="overlay_cond">
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
238 <param name="overlay_selection" value="yes_overlay"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
239 <repeat name="colours">
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
240 <param name="feature_color" value="#ff00ff"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
241 </repeat>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
242 <repeat name="colours">
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="feature_color" value="#1f497d"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
244 </repeat>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
245 <repeat name="colours">
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
246 <param name="feature_color" value="#00b050"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
diff changeset
247 </repeat>
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="legend_position" value="topleft"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 3
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249 </conditional>
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250 <output name="plots" file="Heatmaps_processed.pdf" ftype="pdf" compare="sim_size"/>
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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251 </test>
0
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252 </tests>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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253 <help><![CDATA[
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254
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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255 @CARDINAL_DESCRIPTION@
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256
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257 -----
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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258
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259 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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260
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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261 @MSIDATA_INPUT_DESCRIPTION@
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262
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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263 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
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264
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265
0
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266 **Tips**
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267
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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268 - 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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269 - 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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270
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271 **Output**
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272
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273 - Single Pdf with the heatmap images
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274 - optional: svg file with the heatmap of the first valid m/z in the tabular file
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275
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276
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277 ]]>
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278 </help>
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279 <expand macro="citations"/>
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280 </tool>