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comparison SpectraFilterNormalizer.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="SpectraFilterNormalizer" name="SpectraFilterNormalizer" 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>Applies thresholdfilter to peak spectra.</description> 3 <!--Proposed Tool Section: [Identification]-->
4 <macros> 4 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="2.0.0">
5 <token name="@EXECUTABLE@">SpectraFilterNormalizer</token> 5 <description>Normalizes intensity of peak spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SpectraFilterNormalizer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SpectraFilterNormalizer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraFilterNormalizer
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -threads \${GALAXY_SLOTS:-24} 17 #end if
15 -algorithm:method ${param_method} 18 #if $param_out:
19 -out $param_out
20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_method:
23 -algorithm:method
24 #if &quot; &quot; in str($param_algorithm_method):
25 &quot;$param_algorithm_method&quot;
26 #else
27 $param_algorithm_method
28 #end if
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
16 </command> 35 </command>
17 <inputs> 36 <inputs>
18 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/> 37 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
19 <param name="param_method" type="select" optional="True" value="to_one" label="Normalize by deviding though the TIC ('to_TIC') or normalize to max intensity of one ('to_one')." help="(-method)"> 38 <param help="(-method) intensity of one ('to_one') per spectrum" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" name="param_algorithm_method" optional="True" type="select" value="to_one">
20 <option value="to_one">to_one</option> 39 <option value="to_one">to_one</option>
21 <option value="to_TIC">to_TIC</option> 40 <option value="to_TIC">to_TIC</option>
22 </param> 41 </param>
23 </inputs> 42 <expand macro="advanced_options">
24 <outputs> 43 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
25 <data name="param_out" label="output file " format="mzML"/> 44 </expand>
26 </outputs> 45 </inputs>
27 <help>**What it does** 46 <outputs>
28 47 <data format="mzml" name="param_out"/>
29 Applies thresholdfilter to peak spectra. 48 </outputs>
49 <help>Normalizes intensity of peak spectra.
30 50
31 51
32 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html 52 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html</help>
33 53 </tool>
34 @REFERENCES@
35 </help>
36 </tool>