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<div class="title">ImageCreator </div> </div>
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<div class="textblock"><p>Transforms an LC-MS map into a png image.</p>
<p>The input is first resampled into a matrix using bilinear forward resampling. Then the content of the matrix is written to an image file. The output has a uniform spacing in both dimensions regardless of the input.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
ImageCreator -- Transforms an LC-MS map into an image.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
ImageCreator <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzML')
-in_featureXML <file> Input file (valid formats: 'featureXML')
-out <file>* Output file (valid formats: 'png', 'jpg', 'bmp', 'tiff', 'ppm')
-out_type <file type> The image format. Set this if you want to force a format not reflected by the
'out' filename. (valid: 'png', 'jpg', 'bmp', 'tiff', 'ppm')
-width <number> Number of pixels in m/z dimension.
If 0, one pixel per Th. (default: '1024' min: '0')
-height <number> Number of pixels in RT dimension.
If 0, one pixel per spectrum. (default: '1024' min: '0')
-background_color <color> Background color e.g.: "#FF0000" to choose red as background color (default:
'#FFFFFF')
-feature_color <color> Feature color e.g.: "#00FF00" to choose green as feature color (default: '#00000
0')
-gradient <gradient> Intensity gradient that defines colors for the range between 0 and 100.
Example: '0,#FFFFFF;50,#FF0000;100,#000000'
-max_intensity <int> Maximum peak intensity used to determine range for colors.
If 0, this is determined from the data. (default: '0')
-log_intensity Apply logarithm to intensity values
-transpose Flag to transpose the resampled matrix (RT vs. m/z).
Per default, dimensions run bottom-up in RT and left-right in m/z.
-precursors Mark locations of MS2 precursors.
-precursor_color <color> Color for precursor marks (color code or word, e.g. 'black') (requires 'precurso
rs' flag to be active) (default: '#000000')
-precursor_size <number> Size of the precursor marks (requires 'precursors' flag to be active) (default:
'2' min: '1' max: '3')
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+ImageCreator</span><span class="node_description">Transforms an LC-MS map into an image.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'ImageCreator'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">in_featureXML</span><span class="item_value"></span>
<span class="item_description">input file </span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.png,*.jpg,*.bmp,*.tiff,*.ppm</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_type</span><span class="item_value"></span>
<span class="item_description">The image format. Set this if you want to force a format not reflected by the 'out' filename.</span><span class="item_tags"></span><span class="item_restrictions">png,jpg,bmp,tiff,ppm</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">width</span><span class="item_value">1024</span>
<span class="item_description">Number of pixels in m/z dimension.<br>If 0, one pixel per Th.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">height</span><span class="item_value">1024</span>
<span class="item_description">Number of pixels in RT dimension.<br>If 0, one pixel per spectrum.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">background_color</span><span class="item_value">#FFFFFF</span>
<span class="item_description">Background color e.g.: "#FF0000" to choose red as background color</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">feature_color</span><span class="item_value">#000000</span>
<span class="item_description">Feature color e.g.: "#00FF00" to choose green as feature color</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">gradient</span><span class="item_value"></span>
<span class="item_description">Intensity gradient that defines colors for the range between 0 and 100.<br>Example: '0,#FFFFFF;50,#FF0000;100,#000000'</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_intensity</span><span class="item_value">0</span>
<span class="item_description">Maximum peak intensity used to determine range for colors.<br>If 0, this is determined from the data.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">log_intensity</span><span class="item_value">false</span>
<span class="item_description">Apply logarithm to intensity values</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">transpose</span><span class="item_value">false</span>
<span class="item_description">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.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursors</span><span class="item_value">false</span>
<span class="item_description">Mark locations of MS2 precursors.<br></span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_color</span><span class="item_value">#000000</span>
<span class="item_description">Color for precursor marks (color code or word, e.g. 'black') (requires 'precursors' flag to be active)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_size</span><span class="item_value">2</span>
<span class="item_description">Size of the precursor marks (requires 'precursors' flag to be active)</span><span class="item_tags"></span><span class="item_restrictions">1:3</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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