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comparison ConsensusMapNormalizer.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.0.0">
3 <description>Normalizes maps of one consensusXML file</description>
4 <macros>
5 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>ConsensusMapNormalizer
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_algorithm_type:
19 -algorithm_type
20 #if " " in str($param_algorithm_type):
21 "$param_algorithm_type"
22 #else
23 $param_algorithm_type
24 #end if
25 #end if
26 #if $param_ratio_threshold:
27 -ratio_threshold $param_ratio_threshold
28 #end if
29 -threads \${GALAXY_SLOTS:-24}
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="consensusxml" optional="False" label="input file" help="(-in) "/>
38 <param name="param_algorithm_type" type="select" optional="True" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) ">
39 <option value="robust_regression">robust_regression</option>
40 <option value="median">median</option>
41 <option value="quantile">quantile</option>
42 </param>
43 <param name="param_ratio_threshold" type="float" min="0.001" max="1.0" optional="True" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help="(-ratio_threshold) "/>
44 <expand macro="advanced_options">
45 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
46 </expand>
47 </inputs>
48 <outputs>
49 <data name="param_out" format="consensusxml"/>
50 </outputs>
51 <help>**What it does**
52
53 Normalizes maps of one consensusXML file
54
55
56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help>
57 <expand macro="references"/>
58 </tool>