diff ImageCreator.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ImageCreator.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,67 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="ImageCreator" name="ImageCreator" version="1.12.0">
+  <description>Transforms an LC-MS map into an image.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ImageCreator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ImageCreator
+
+-in ${param_in}
+-in_featureXML ${param_in_featureXML}
+-out ${param_out}
+-out_type ${param_out_type}
+-width ${param_width}
+-height ${param_height}
+-background_color ${param_background_color}
+-feature_color ${param_feature_color}
+-gradient ${param_gradient}
+-max_intensity ${param_max_intensity}
+${param_log_intensity}
+${param_transpose}
+${param_precursors}
+-precursor_color ${param_precursor_color}
+-precursor_size ${param_precursor_size}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
+    <param name="param_in_featureXML" type="data" format="featureXML" optional="True" label="input file " help="(-in_featureXML)"/>
+    <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)">
+      <option value="png">png</option>
+      <option value="jpg">jpg</option>
+      <option value="bmp">bmp</option>
+      <option value="tiff">tiff</option>
+      <option value="ppm">ppm</option>
+    </param>
+    <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)"/>
+    <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)"/>
+    <param name="param_background_color" type="text" size="20" value="#FFFFFF" label="Background color e.g.: &quot;#FF0000&quot; to choose red as background color" help="(-background_color)"/>
+    <param name="param_feature_color" type="text" size="20" value="#000000" label="Feature color e.g.: &quot;#00FF00&quot; to choose green as feature color" help="(-feature_color)"/>
+    <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)"/>
+    <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)"/>
+    <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)"/>
+    <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)"/>
+    <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)"/>
+    <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)"/>
+    <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)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="jpg">
+      <change_format>
+        <when input="param_out_type" value="png" format="png"/>
+      </change_format>
+    </data>
+  </outputs>
+  <help>**What it does**
+
+Transforms an LC-MS map into an image.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ImageCreator.html
+
+@REFERENCES@
+</help>
+</tool>