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comparison ConsensusMapNormalizer.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
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" 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>Normalizes maps of one consensusXML file</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.0.0">
5 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token> 5 <description>Normalizes maps of one consensusXML file</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>ConsensusMapNormalizer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ConsensusMapNormalizer
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -algorithm_type ${param_algorithm_type} 17 #end if
15 -ratio_threshold ${param_ratio_threshold} 18 #if $param_out:
16 -threads \${GALAXY_SLOTS:-24} 19 -out $param_out
20 #end if
21 #if $param_algorithm_type:
22 -algorithm_type
23 #if &quot; &quot; in str($param_algorithm_type):
24 &quot;$param_algorithm_type&quot;
25 #else
26 $param_algorithm_type
27 #end if
28 #end if
29 #if $param_ratio_threshold:
30 -ratio_threshold $param_ratio_threshold
31 #end if
32 -threads \${GALAXY_SLOTS:-24}
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #end if
17 </command> 38 </command>
18 <inputs> 39 <inputs>
19 <param name="param_in" type="data" format="consensusXML" optional="False" label="input file" help="(-in)"/> 40 <param format="consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
20 <param name="param_algorithm_type" type="select" optional="True" value="robust_regression" label="The normalization algorithm that is applied." help="(-algorithm_type)"> 41 <param help="(-algorithm_type) " label="The normalization algorithm that is applied" name="param_algorithm_type" optional="True" type="select" value="robust_regression">
21 <option value="robust_regression">robust_regression</option> 42 <option value="robust_regression">robust_regression</option>
22 <option value="median">median</option> 43 <option value="median">median</option>
23 <option value="quantile">quantile</option> 44 <option value="quantile">quantile</option>
24 </param> 45 </param>
25 <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)"/> 46 <param help="(-ratio_threshold) " 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" max="1.0" min="0.001" name="param_ratio_threshold" optional="True" type="float" value="0.67"/>
26 </inputs> 47 <expand macro="advanced_options">
27 <outputs> 48 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
28 <data name="param_out" label="output file" format="consensusXML"/> 49 </expand>
29 </outputs> 50 </inputs>
30 <help>**What it does** 51 <outputs>
31 52 <data format="consensusxml" name="param_out"/>
32 Normalizes maps of one consensusXML file 53 </outputs>
54 <help>Normalizes maps of one consensusXML file
33 55
34 56
35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html 57 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help>
36 58 </tool>
37 @REFERENCES@
38 </help>
39 </tool>