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comparison BaselineFilter.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="BaselineFilter" name="BaselineFilter" version="1.12.0">
3 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
4 <macros>
5 <token name="@EXECUTABLE@">BaselineFilter</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>BaselineFilter
11
12 -in ${param_in}
13 -out ${param_out}
14 -struc_elem_length ${param_struc_elem_length}
15 -struc_elem_unit ${param_struc_elem_unit}
16 -method ${param_method}
17 -threads \${GALAXY_SLOTS:-24}
18 </command>
19 <inputs>
20 <param name="param_in" type="data" format="mzML" optional="False" label="input raw data file " help="(-in)"/>
21 <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)." help="(-struc_elem_length)"/>
22 <param name="param_struc_elem_unit" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' parameter." help="(-struc_elem_unit)">
23 <option value="Thomson">Thomson</option>
24 <option value="DataPoints">DataPoints</option>
25 </param>
26 <param name="param_method" type="select" optional="True" value="tophat" label="The name of the morphological filter to be applied. If you are unsure, use the default." help="(-method)">
27 <option value="identity">identity</option>
28 <option value="erosion">erosion</option>
29 <option value="dilation">dilation</option>
30 <option value="opening">opening</option>
31 <option value="closing">closing</option>
32 <option value="gradient">gradient</option>
33 <option value="tophat">tophat</option>
34 <option value="bothat">bothat</option>
35 <option value="erosion_simple">erosion_simple</option>
36 <option value="dilation_simple">dilation_simple</option>
37 </param>
38 </inputs>
39 <outputs>
40 <data name="param_out" label="output raw data file " format="mzML"/>
41 </outputs>
42 <help>**What it does**
43
44 Removes the baseline from profile spectra using a top-hat filter.
45
46
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html
48
49 @REFERENCES@
50 </help>
51 </tool>