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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="1.12.0">
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3 <description>Groups corresponding isotope-labeled features in a feature map.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FeatureLinkerLabeled
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -threads \${GALAXY_SLOTS:-24}
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15 ${param_rt_estimate}
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16 -algorithm:rt_pair_dist ${param_rt_pair_dist}
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17 -algorithm:rt_dev_low ${param_rt_dev_low}
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18 -algorithm:rt_dev_high ${param_rt_dev_high}
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19 -algorithm:mz_pair_dists ${param_mz_pair_dists}
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20 -algorithm:mz_dev ${param_mz_dev}
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21 #if $adv_opts.adv_opts_selector=='advanced':
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22 ${adv_opts.param_mrm}
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="param_in" type="data" format="featureXML" optional="False" label="Input file" help="(-in)"/>
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27 <param name="param_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate true" falsevalue="-algorithm:rt_estimate false" checked="true" optional="True" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance." help="(-rt_estimate)"/>
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28 <param name="param_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist)"/>
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29 <param name="param_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low)"/>
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30 <param name="param_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high)"/>
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31 <param name="param_mz_pair_dists" type="text" size="20" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)" help="(-mz_pair_dists)"/>
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32 <param name="param_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance#br#" help="(-mz_dev)"/>
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33 <expand macro="advanced_options">
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34 <param name="param_mrm" type="boolean" truevalue="-algorithm:mrm true" falsevalue="-algorithm:mrm false" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm)"/>
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35 </expand>
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36 </inputs>
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37 <outputs>
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38 <data name="param_out" label="Output file" format="consensusXML"/>
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39 </outputs>
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40 <help>**What it does**
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41
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42 Groups corresponding isotope-labeled features in a feature map.
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43
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44
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45 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html
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46
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47 @REFERENCES@
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48 </help>
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49 </tool>
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