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comparison BaselineFilter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="BaselineFilter" name="BaselineFilter" version="1.12.0"> 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 <description>Removes the baseline from profile spectra using a top-hat filter.</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="BaselineFilter" name="BaselineFilter" version="2.0.0">
5 <token name="@EXECUTABLE@">BaselineFilter</token> 5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">BaselineFilter</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>BaselineFilter 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>BaselineFilter
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -struc_elem_length ${param_struc_elem_length} 17 #end if
15 -struc_elem_unit ${param_struc_elem_unit} 18 #if $param_out:
16 -method ${param_method} 19 -out $param_out
17 -threads \${GALAXY_SLOTS:-24} 20 #end if
21 #if $param_struc_elem_length:
22 -struc_elem_length $param_struc_elem_length
23 #end if
24 #if $param_struc_elem_unit:
25 -struc_elem_unit
26 #if &quot; &quot; in str($param_struc_elem_unit):
27 &quot;$param_struc_elem_unit&quot;
28 #else
29 $param_struc_elem_unit
30 #end if
31 #end if
32 #if $param_method:
33 -method
34 #if &quot; &quot; in str($param_method):
35 &quot;$param_method&quot;
36 #else
37 $param_method
38 #end if
39 #end if
40 -threads \${GALAXY_SLOTS:-24}
41 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force:
43 -force
44 #end if
45 #end if
18 </command> 46 </command>
19 <inputs> 47 <inputs>
20 <param name="param_in" type="data" format="mzML" optional="False" label="input raw data file " help="(-in)"/> 48 <param format="mzml" help="(-in) " label="input raw data file" name="param_in" optional="False" type="data"/>
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)"/> 49 <param help="(-struc_elem_length) " label="Length of the structuring element (should be wider than maximal peak width - see documentation)" name="param_struc_elem_length" type="float" value="3.0"/>
22 <param name="param_struc_elem_unit" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' parameter." help="(-struc_elem_unit)"> 50 <param help="(-struc_elem_unit) " label="Unit of 'struc_elem_length' paramete" name="param_struc_elem_unit" optional="True" type="select" value="Thomson">
23 <option value="Thomson">Thomson</option> 51 <option value="Thomson">Thomson</option>
24 <option value="DataPoints">DataPoints</option> 52 <option value="DataPoints">DataPoints</option>
25 </param> 53 </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)"> 54 <param help="(-method) If you are unsure, use the default" label="The name of the morphological filter to be applied" name="param_method" optional="True" type="select" value="tophat">
27 <option value="identity">identity</option> 55 <option value="identity">identity</option>
28 <option value="erosion">erosion</option> 56 <option value="erosion">erosion</option>
29 <option value="dilation">dilation</option> 57 <option value="dilation">dilation</option>
30 <option value="opening">opening</option> 58 <option value="opening">opening</option>
31 <option value="closing">closing</option> 59 <option value="closing">closing</option>
32 <option value="gradient">gradient</option> 60 <option value="gradient">gradient</option>
33 <option value="tophat">tophat</option> 61 <option value="tophat">tophat</option>
34 <option value="bothat">bothat</option> 62 <option value="bothat">bothat</option>
35 <option value="erosion_simple">erosion_simple</option> 63 <option value="erosion_simple">erosion_simple</option>
36 <option value="dilation_simple">dilation_simple</option> 64 <option value="dilation_simple">dilation_simple</option>
37 </param> 65 </param>
38 </inputs> 66 <expand macro="advanced_options">
39 <outputs> 67 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
40 <data name="param_out" label="output raw data file " format="mzML"/> 68 </expand>
41 </outputs> 69 </inputs>
42 <help>**What it does** 70 <outputs>
43 71 <data format="mzml" name="param_out"/>
44 Removes the baseline from profile spectra using a top-hat filter. 72 </outputs>
73 <help>Removes the baseline from profile spectra using a top-hat filter.
45 74
46 75
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html 76 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help>
48 77 </tool>
49 @REFERENCES@
50 </help>
51 </tool>