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annotate 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
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6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MRMPairFinder" name="MRMPairFinder" version="2.0.0">
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5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MRMPairFinder</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>MRMPairFinder
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_pair_in:
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19 -pair_in $param_pair_in
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_feature_out:
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25 -feature_out $param_feature_out
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_mass_tolerance:
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30 -mass_tolerance $adv_opts.param_mass_tolerance
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31 #end if
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32 #if $adv_opts.param_RT_tolerance:
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33 -RT_tolerance $adv_opts.param_RT_tolerance
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34 #end if
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35 #if $adv_opts.param_RT_pair_tolerance:
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36 -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
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37 #end if
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38 #if $adv_opts.param_force:
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39 -force
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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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"/>
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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"/>
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46 <expand macro="advanced_options">
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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"/>
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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"/>
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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"/>
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50 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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51 </expand>
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52 </inputs>
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53 <outputs>
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54 <data format="consensusxml" name="param_out"/>
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55 <data format="xml" name="param_feature_out"/>
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56 </outputs>
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57 <help>Util which can be used to evaluate labeled pair ratios on MRM features.
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58
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59
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60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html</help>
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61 </tool>