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comparison MRMPairFinder.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="MRMPairFinder" name="MRMPairFinder" 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>Util which can be used to evaluate labeled pair ratios on MRM features.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="MRMPairFinder" name="MRMPairFinder" version="2.0.0">
5 <token name="@EXECUTABLE@">MRMPairFinder</token> 5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MRMPairFinder</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MRMPairFinder 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MRMPairFinder
11 14
12 -in ${param_in} 15 #if $param_in:
13 -pair_in ${param_pair_in} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 -feature_out ${param_feature_out} 18 #if $param_pair_in:
16 -threads \${GALAXY_SLOTS:-24} 19 -pair_in $param_pair_in
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_feature_out:
25 -feature_out $param_feature_out
26 #end if
27 -threads \${GALAXY_SLOTS:-24}
17 #if $adv_opts.adv_opts_selector=='advanced': 28 #if $adv_opts.adv_opts_selector=='advanced':
18 -mass_tolerance ${adv_opts.param_mass_tolerance} 29 #if $adv_opts.param_mass_tolerance:
19 -RT_tolerance ${adv_opts.param_RT_tolerance} 30 -mass_tolerance $adv_opts.param_mass_tolerance
20 -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance} 31 #end if
32 #if $adv_opts.param_RT_tolerance:
33 -RT_tolerance $adv_opts.param_RT_tolerance
34 #end if
35 #if $adv_opts.param_RT_pair_tolerance:
36 -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
37 #end if
38 #if $adv_opts.param_force:
39 -force
40 #end if
21 #end if 41 #end if
22 </command> 42 </command>
23 <inputs> 43 <inputs>
24 <param name="param_in" type="data" format="featureXML" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra." help="(-in)"/> 44 <param format="xml" help="(-in) " label="Input featureXML file containing the features of the MRM experiment spectra" name="param_in" optional="False" type="data"/>
25 <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in)"/> 45 <param format="tabular" help="(-pair_in) " label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" name="param_pair_in" optional="False" type="data"/>
26 <expand macro="advanced_options"> 46 <expand macro="advanced_options">
27 <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-mass_tolerance)"/> 47 <param help="(-mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_mass_tolerance" optional="True" type="float" value="0.01"/>
28 <param name="param_RT_tolerance" type="float" min="0.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file." help="(-RT_tolerance)"/> 48 <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="0.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
29 <param name="param_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have." help="(-RT_pair_tolerance)"/> 49 <param help="(-RT_pair_tolerance) " label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" min="0.0" name="param_RT_pair_tolerance" optional="True" type="float" value="5.0"/>
30 </expand> 50 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
31 </inputs> 51 </expand>
32 <outputs> 52 </inputs>
33 <data name="param_out" label="Output consensusXML file were the pairs of the features will be written to." format="consensusXML"/> 53 <outputs>
34 <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/> 54 <data format="consensusxml" name="param_out"/>
35 </outputs> 55 <data format="xml" name="param_feature_out"/>
36 <help>**What it does** 56 </outputs>
37 57 <help>Util which can be used to evaluate labeled pair ratios on MRM features.
38 Util which can be used to evaluate labeled pair ratios on MRM features.
39 58
40 59
41 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html 60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html</help>
42 61 </tool>
43 @REFERENCES@
44 </help>
45 </tool>