Mercurial > repos > galaxyp > openms_featurelinkerlabeled

annotate FeatureLinkerLabeled.xml @ 0:2fe5ef9f1760 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:45:07 -0500
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2fe5ef9f1760 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="2.1.0">
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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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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_out:
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19 -out $param_out
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20 #end if
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21 #if $param_algorithm_rt_estimate:
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22 -algorithm:rt_estimate $param_algorithm_rt_estimate
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23 #end if
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24 #if $param_algorithm_rt_pair_dist:
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25 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
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26 #end if
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27 #if $param_algorithm_rt_dev_low:
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28 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
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29 #end if
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30 #if $param_algorithm_rt_dev_high:
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31 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
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32 #end if
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33
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34 #if $rep_param_algorithm_mz_pair_dists:
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35 -algorithm:mz_pair_dists
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36 #for token in $rep_param_algorithm_mz_pair_dists:
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37 #if " " in str(token):
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38 "$token.param_algorithm_mz_pair_dists"
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39 #else
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40 $token.param_algorithm_mz_pair_dists
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41 #end if
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42 #end for
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43 #end if
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44 #if $param_algorithm_mz_dev:
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45 -algorithm:mz_dev $param_algorithm_mz_dev
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46 #end if
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47 #if $adv_opts.adv_opts_selector=='advanced':
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48 #if $adv_opts.param_force:
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49 -force
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50 #end if
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51 #if $adv_opts.param_algorithm_mrm:
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52 -algorithm:mrm
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53 #end if
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54 #end if
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55 </command>
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56 <inputs>
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57 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/>
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58 <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" 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">
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59 <option value="true" selected="true">true</option>
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60 <option value="false">false</option>
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61 </param>
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62 <param name="param_algorithm_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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63 <param name="param_algorithm_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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64 <param name="param_algorithm_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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65 <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
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66 <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
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67 <sanitizer>
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68 <valid initial="string.printable">
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69 <remove value="'"/>
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70 <remove value="&quot;"/>
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71 </valid>
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72 </sanitizer>
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73 </param>
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74 </repeat>
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75 <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
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76 <expand macro="advanced_options">
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77 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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78 <param name="param_algorithm_mrm" display="radio" type="boolean" truevalue="-algorithm:mrm" falsevalue="" 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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79 </expand>
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80 </inputs>
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81 <outputs>
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82 <data name="param_out" format="consensusxml"/>
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83 </outputs>
2fe5ef9f1760 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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84 <help>Groups corresponding isotope-labeled features in a feature map.
2fe5ef9f1760 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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85
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86
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87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
2fe5ef9f1760 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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88 </tool>