annotate MultiplexResolver.xml @ 6:7b9dd0796558 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 15:09:44 -0400
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children 8023d63040f6
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MultiplexResolver" name="MultiplexResolver" version="2.3.0">
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5 <description>Completes peptide multiplets and resolves conflicts within them.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MultiplexResolver</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>MultiplexResolver
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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_out_conflicts:
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22 -out_conflicts $param_out_conflicts
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23 #end if
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24 #if $param_algorithm_labels:
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25 -algorithm:labels "$param_algorithm_labels"
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26 #end if
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27 #if $param_algorithm_missed_cleavages:
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28 -algorithm:missed_cleavages $param_algorithm_missed_cleavages
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29 #end if
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_force:
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32 -force
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33 #end if
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34 #if $adv_opts.param_algorithm_mass_tolerance:
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35 -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance
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36 #end if
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37 #if $adv_opts.param_labels_Arg6:
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38 -labels:Arg6 $adv_opts.param_labels_Arg6
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39 #end if
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40 #if $adv_opts.param_labels_Arg10:
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41 -labels:Arg10 $adv_opts.param_labels_Arg10
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42 #end if
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43 #if $adv_opts.param_labels_Lys4:
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44 -labels:Lys4 $adv_opts.param_labels_Lys4
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45 #end if
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46 #if $adv_opts.param_labels_Lys6:
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47 -labels:Lys6 $adv_opts.param_labels_Lys6
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48 #end if
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49 #if $adv_opts.param_labels_Lys8:
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50 -labels:Lys8 $adv_opts.param_labels_Lys8
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51 #end if
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52 #if $adv_opts.param_labels_Leu3:
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53 -labels:Leu3 $adv_opts.param_labels_Leu3
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54 #end if
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55 #if $adv_opts.param_labels_Dimethyl0:
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56 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
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57 #end if
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58 #if $adv_opts.param_labels_Dimethyl4:
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59 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
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60 #end if
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61 #if $adv_opts.param_labels_Dimethyl6:
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62 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
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63 #end if
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64 #if $adv_opts.param_labels_Dimethyl8:
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65 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
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66 #end if
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67 #if $adv_opts.param_labels_ICPL0:
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68 -labels:ICPL0 $adv_opts.param_labels_ICPL0
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69 #end if
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70 #if $adv_opts.param_labels_ICPL4:
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71 -labels:ICPL4 $adv_opts.param_labels_ICPL4
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72 #end if
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73 #if $adv_opts.param_labels_ICPL6:
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74 -labels:ICPL6 $adv_opts.param_labels_ICPL6
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75 #end if
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76 #if $adv_opts.param_labels_ICPL10:
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77 -labels:ICPL10 $adv_opts.param_labels_ICPL10
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78 #end if
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79 #end if
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80 </command>
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81 <inputs>
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82 <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" help="(-in) "/>
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83 <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
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84 <sanitizer>
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85 <valid initial="string.printable">
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86 <remove value="'"/>
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87 <remove value="&quot;"/>
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88 </valid>
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89 </sanitizer>
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90 </param>
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91 <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
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92 <expand macro="advanced_options">
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93 <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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94 <param name="param_algorithm_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/>
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95 <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/>
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96 <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/>
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97 <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/>
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98 <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/>
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99 <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/>
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100 <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/>
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101 <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/>
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102 <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/>
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103 <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/>
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104 <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/>
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105 <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/>
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106 <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/>
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107 <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/>
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108 <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/>
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109 </expand>
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110 </inputs>
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111 <outputs>
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112 <data name="param_out" format="consensusxml"/>
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113 <data name="param_out_conflicts" format="consensusxml"/>
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114 </outputs>
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115 <help>Completes peptide multiplets and resolves conflicts within them.
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116
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117
1
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118 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MultiplexResolver.html</help>
0
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119 </tool>