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annotate FeatureLinkerLabeled.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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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: [Map Alignment]-->
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4 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.0.0">
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5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</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>FeatureLinkerLabeled
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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_out:
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19 -out $param_out
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20 #end if
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21 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_rt_estimate:
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23 -algorithm:rt_estimate
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24 #end if
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25 #if $param_algorithm_rt_pair_dist:
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26 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
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27 #end if
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28 #if $param_algorithm_rt_dev_low:
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29 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
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30 #end if
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31 #if $param_algorithm_rt_dev_high:
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32 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
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33 #end if
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35 #if $rep_param_algorithm_mz_pair_dists:
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36 -algorithm:mz_pair_dists
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37 #for token in $rep_param_algorithm_mz_pair_dists:
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38 #if &quot; &quot; in str(token):
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39 &quot;$token.param_algorithm_mz_pair_dists&quot;
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40 #else
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41 $token.param_algorithm_mz_pair_dists
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42 #end if
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43 #end for
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44 #end if
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45 #if $param_algorithm_mz_dev:
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46 -algorithm:mz_dev $param_algorithm_mz_dev
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47 #end if
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48 #if $adv_opts.adv_opts_selector=='advanced':
4
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #if $adv_opts.param_algorithm_mrm:
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53 -algorithm:mrm
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54 #end if
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55 #end if
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56 </command>
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57 <inputs>
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58 <param format="xml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
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59 <param checked="true" falsevalue="" help="(-rt_estimate) 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" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" name="param_algorithm_rt_estimate" optional="True" truevalue="-algorithm:rt_estimate" type="boolean"/>
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60 <param help="(-rt_pair_dist) " label="optimal pair distance in RT [sec] from light to heavy feature" name="param_algorithm_rt_pair_dist" type="float" value="-20.0"/>
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61 <param help="(-rt_dev_low) " label="maximum allowed deviation below optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_low" optional="True" type="float" value="15.0"/>
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62 <param help="(-rt_dev_high) " label="maximum allowed deviation above optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_high" optional="True" type="float" value="15.0"/>
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63 <repeat max="1" min="0" name="rep_param_algorithm_mz_pair_dists" title="param_algorithm_mz_pair_dists">
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64 <param help="(-mz_pair_dists) by division through charge)" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." name="param_algorithm_mz_pair_dists" size="30" type="text" value="4.0">
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65 <sanitizer>
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66 <valid initial="string.printable">
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67 <remove value="'"/>
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68 <remove value="&quot;"/>
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69 </valid>
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70 </sanitizer>
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71 </param>
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72 </repeat>
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73 <param help="(-mz_dev) " label="maximum allowed deviation from optimal m/z distance" min="0.0" name="param_algorithm_mz_dev" optional="True" type="float" value="0.05"/>
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74 <expand macro="advanced_options">
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75 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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76 <param checked="false" falsevalue="" help="(-mrm) " label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" name="param_algorithm_mrm" optional="True" truevalue="-algorithm:mrm" type="boolean"/>
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77 </expand>
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78 </inputs>
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79 <outputs>
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80 <data format="consensusxml" name="param_out"/>
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81 </outputs>
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82 <help>Groups corresponding isotope-labeled features in a feature map.
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83
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84
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85 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
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86 </tool>