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comparison BaselineFilter.xml @ 0:4768c361b11f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 13:01:28 -0500
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children 4e3ec1e5783f
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-1:000000000000 0:4768c361b11f
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="BaselineFilter" name="BaselineFilter" version="2.1.0">
5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
6 <macros>
7 <token name="@EXECUTABLE@">BaselineFilter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>BaselineFilter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_struc_elem_length:
22 -struc_elem_length $param_struc_elem_length
23 #end if
24 #if $param_struc_elem_unit:
25 -struc_elem_unit $param_struc_elem_unit
26 #end if
27 #if $param_method:
28 -method $param_method
29 #end if
30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force:
32 -force
33 #end if
34 #end if
35 </command>
36 <inputs>
37 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
38 <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) "/>
39 <param name="param_struc_elem_unit" display="radio" type="select" optional="False" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) ">
40 <option value="Thomson" selected="true">Thomson</option>
41 <option value="DataPoints">DataPoints</option>
42 </param>
43 <param name="param_method" type="select" optional="False" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default">
44 <option value="identity">identity</option>
45 <option value="erosion">erosion</option>
46 <option value="dilation">dilation</option>
47 <option value="opening">opening</option>
48 <option value="closing">closing</option>
49 <option value="gradient">gradient</option>
50 <option value="tophat" selected="true">tophat</option>
51 <option value="bothat">bothat</option>
52 <option value="erosion_simple">erosion_simple</option>
53 <option value="dilation_simple">dilation_simple</option>
54 </param>
55 <expand macro="advanced_options">
56 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
57 </expand>
58 </inputs>
59 <outputs>
60 <data name="param_out" format="mzml"/>
61 </outputs>
62 <help>Removes the baseline from profile spectra using a top-hat filter.
63
64
65 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help>
66 </tool>