Mercurial > repos > galaxyp > openms_consensusmapnormalizer

comparison ConsensusMapNormalizer.xml @ 12:6c3d3db54b1f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:53:47 -0400
parents 4fec36da6f53
children 6254b3dc8c93
comparison
equal deleted inserted replaced
11:4b11097c84d4 12:6c3d3db54b1f
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Map Alignment]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.2.0"> 4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.3.0">
5 <description>Normalizes maps of one consensusXML file</description> 5 <description>Normalizes maps of one consensusXML file</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token> 7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>ConsensusMapNormalizer 13 <command detect_errors="aggressive"><![CDATA[ConsensusMapNormalizer
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
38 #end if 38 #end if
39 #if $adv_opts.param_force: 39 #if $adv_opts.param_force:
40 -force 40 -force
41 #end if 41 #end if
42 #end if 42 #end if
43 </command> 43 ]]></command>
44 <inputs> 44 <inputs>
45 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file" help="(-in) "/> 45 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file" help="(-in) "/>
46 <param name="param_algorithm_type" display="radio" type="select" optional="False" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)"> 46 <param name="param_algorithm_type" display="radio" type="select" optional="False" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
47 <option value="robust_regression" selected="true">robust_regression</option> 47 <option value="robust_regression" selected="true">robust_regression</option>
48 <option value="median">median</option> 48 <option value="median">median</option>
74 <data name="param_out" format="consensusxml"/> 74 <data name="param_out" format="consensusxml"/>
75 </outputs> 75 </outputs>
76 <help>Normalizes maps of one consensusXML file 76 <help>Normalizes maps of one consensusXML file
77 77
78 78
79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help> 79 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ConsensusMapNormalizer.html</help>
80 </tool> 80 </tool>