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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ImageCreator" name="ImageCreator" version="1.12.0">
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3 <description>Transforms an LC-MS map into an image.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ImageCreator</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ImageCreator
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11
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12 -in ${param_in}
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13 -in_featureXML ${param_in_featureXML}
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14 -out ${param_out}
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15 -out_type ${param_out_type}
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16 -width ${param_width}
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17 -height ${param_height}
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18 -background_color ${param_background_color}
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19 -feature_color ${param_feature_color}
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20 -gradient ${param_gradient}
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21 -max_intensity ${param_max_intensity}
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22 ${param_log_intensity}
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23 ${param_transpose}
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24 ${param_precursors}
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25 -precursor_color ${param_precursor_color}
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26 -precursor_size ${param_precursor_size}
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27 -threads \${GALAXY_SLOTS:-24}
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28 </command>
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29 <inputs>
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30 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
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31 <param name="param_in_featureXML" type="data" format="featureXML" optional="True" label="input file " help="(-in_featureXML)"/>
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32 <param name="param_out_type" type="select" optional="True" label="The image format. Set this if you want to force a format not reflected by the 'out' filename." help="(-out_type)">
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33 <option value="png">png</option>
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34 <option value="jpg">jpg</option>
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35 <option value="bmp">bmp</option>
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36 <option value="tiff">tiff</option>
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37 <option value="ppm">ppm</option>
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38 </param>
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39 <param name="param_width" type="integer" min="0" optional="True" value="1024" label="Number of pixels in m/z dimension.#br#If 0, one pixel per Th." help="(-width)"/>
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40 <param name="param_height" type="integer" min="0" optional="True" value="1024" label="Number of pixels in RT dimension.#br#If 0, one pixel per spectrum." help="(-height)"/>
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41 <param name="param_background_color" type="text" size="20" value="#FFFFFF" label="Background color e.g.: "#FF0000" to choose red as background color" help="(-background_color)"/>
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42 <param name="param_feature_color" type="text" size="20" value="#000000" label="Feature color e.g.: "#00FF00" to choose green as feature color" help="(-feature_color)"/>
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43 <param name="param_gradient" type="text" size="20" label="Intensity gradient that defines colors for the range between 0 and 100.#br#Example: '0,#FFFFFF;50,#FF0000;100,#000000'" help="(-gradient)"/>
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44 <param name="param_max_intensity" type="float" value="0.0" label="Maximum peak intensity used to determine range for colors.#br#If 0, this is determined from the data." help="(-max_intensity)"/>
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45 <param name="param_log_intensity" type="boolean" truevalue="-log_intensity true" falsevalue="-log_intensity false" checked="false" optional="True" label="Apply logarithm to intensity values" help="(-log_intensity)"/>
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46 <param name="param_transpose" type="boolean" truevalue="-transpose true" falsevalue="-transpose false" checked="false" optional="True" label="flag to transpose the resampled matrix (RT vs. m/z).#br#Per default, dimensions run bottom-up in RT and left-right in m/z." help="(-transpose)"/>
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47 <param name="param_precursors" type="boolean" truevalue="-precursors true" falsevalue="-precursors false" checked="false" optional="True" label="Mark locations of MS2 precursors.#br#" help="(-precursors)"/>
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48 <param name="param_precursor_color" type="text" size="20" value="#000000" label="Color for precursor marks (color code or word, e.g. 'black') (requires 'precursors' flag to be active)" help="(-precursor_color)"/>
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49 <param name="param_precursor_size" type="integer" min="1" max="3" optional="True" value="2" label="Size of the precursor marks (requires 'precursors' flag to be active)" help="(-precursor_size)"/>
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50 </inputs>
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51 <outputs>
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52 <data name="param_out" label="output file" format="jpg">
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53 <change_format>
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54 <when input="param_out_type" value="png" format="png"/>
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55 </change_format>
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56 </data>
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57 </outputs>
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58 <help>**What it does**
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59
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60 Transforms an LC-MS map into an image.
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61
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62
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63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ImageCreator.html
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64
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65 @REFERENCES@
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66 </help>
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67 </tool>
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