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annotate FeatureLinkerUnlabeled.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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4
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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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.0.0">
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5 <description>Groups corresponding features from multiple maps.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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>FeatureLinkerUnlabeled
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_keep_subelements:
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23 -keep_subelements
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24 #end if
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25 -threads \${GALAXY_SLOTS:-24}
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26 #if $param_algorithm_second_nearest_gap:
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27 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
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28 #end if
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29 #if $param_algorithm_use_identifications:
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30 -algorithm:use_identifications
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31 #end if
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32 #if $param_algorithm_ignore_charge:
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33 -algorithm:ignore_charge
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34 #end if
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35 #if $param_algorithm_distance_RT_max_difference:
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36 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
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37 #end if
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38 #if $param_algorithm_distance_MZ_max_difference:
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39 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
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40 #end if
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41 #if $param_algorithm_distance_MZ_unit:
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42 -algorithm:distance_MZ:unit
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43 #if &quot; &quot; in str($param_algorithm_distance_MZ_unit):
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44 &quot;$param_algorithm_distance_MZ_unit&quot;
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45 #else
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46 $param_algorithm_distance_MZ_unit
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47 #end if
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48 #end if
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49 #if $adv_opts.adv_opts_selector=='advanced':
4
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50 #if $adv_opts.param_force:
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51 -force
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52 #end if
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53 #if $adv_opts.param_algorithm_distance_RT_exponent:
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54 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
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55 #end if
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56 #if $adv_opts.param_algorithm_distance_RT_weight:
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57 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
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58 #end if
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59 #if $adv_opts.param_algorithm_distance_MZ_exponent:
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60 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
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61 #end if
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62 #if $adv_opts.param_algorithm_distance_MZ_weight:
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63 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
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64 #end if
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65 #if $adv_opts.param_algorithm_distance_intensity_exponent:
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66 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
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67 #end if
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68 #if $adv_opts.param_algorithm_distance_intensity_weight:
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69 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
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70 #end if
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71 #end if
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72 </command>
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73 <inputs>
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74 <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
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75 <sanitizer>
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76 <valid initial="string.printable">
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77 <remove value="'"/>
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78 <remove value="&quot;"/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/>
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83 <param help="(-second_nearest_gap) " label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" min="1.0" name="param_algorithm_second_nearest_gap" optional="True" type="float" value="2.0"/>
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84 <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" name="param_algorithm_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/>
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85 <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/>
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86 <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
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87 <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
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88 <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da">
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89 <option value="Da">Da</option>
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90 <option value="ppm">ppm</option>
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91 </param>
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92 <expand macro="advanced_options">
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93 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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94 <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_RT_exponent" optional="True" type="float" value="1.0"/>
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95 <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/>
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96 <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
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97 <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/>
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98 <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
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99 <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/>
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100 </expand>
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101 </inputs>
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102 <outputs>
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103 <data format="consensusxml" name="param_out"/>
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104 </outputs>
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105 <help>Groups corresponding features from multiple maps.
0
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106
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107
4
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108 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html</help>
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109 </tool>