Mercurial > repos > galaxyp > openms_baselinefilter
comparison BaselineFilter.xml @ 0:4768c361b11f draft
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 |
parents | |
children | 4e3ec1e5783f |
comparison
equal
deleted
inserted
replaced
-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> |