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annotate Decharger.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
parents 3d84209d3178
children
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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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: [Quantitation]-->
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4 <tool id="Decharger" name="Decharger" version="2.0.0">
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5 <description>Decharges and merges different feature charge variants of the same peptide.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Decharger</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>Decharger
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14
4
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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_cm:
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19 -out_cm $param_out_cm
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20 #end if
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21 #if $param_out_fm:
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22 -out_fm $param_out_fm
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23 #end if
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24 #if $param_outpairs:
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25 -outpairs $param_outpairs
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $param_algorithm_FeatureDeconvolution_charge_min:
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29 -algorithm:FeatureDeconvolution:charge_min $param_algorithm_FeatureDeconvolution_charge_min
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30 #end if
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31 #if $param_algorithm_FeatureDeconvolution_charge_max:
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32 -algorithm:FeatureDeconvolution:charge_max $param_algorithm_FeatureDeconvolution_charge_max
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33 #end if
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34 #if $param_algorithm_FeatureDeconvolution_charge_span_max:
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35 -algorithm:FeatureDeconvolution:charge_span_max $param_algorithm_FeatureDeconvolution_charge_span_max
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36 #end if
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37 #if $param_algorithm_FeatureDeconvolution_q_try:
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38 -algorithm:FeatureDeconvolution:q_try
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39 #if &quot; &quot; in str($param_algorithm_FeatureDeconvolution_q_try):
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40 &quot;$param_algorithm_FeatureDeconvolution_q_try&quot;
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41 #else
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42 $param_algorithm_FeatureDeconvolution_q_try
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43 #end if
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44 #end if
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45 #if $param_algorithm_FeatureDeconvolution_retention_max_diff:
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46 -algorithm:FeatureDeconvolution:retention_max_diff $param_algorithm_FeatureDeconvolution_retention_max_diff
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47 #end if
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48 #if $param_algorithm_FeatureDeconvolution_retention_max_diff_local:
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49 -algorithm:FeatureDeconvolution:retention_max_diff_local $param_algorithm_FeatureDeconvolution_retention_max_diff_local
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50 #end if
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51 #if $param_algorithm_FeatureDeconvolution_mass_max_diff:
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52 -algorithm:FeatureDeconvolution:mass_max_diff $param_algorithm_FeatureDeconvolution_mass_max_diff
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53 #end if
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54
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55 #if $rep_param_algorithm_FeatureDeconvolution_potential_adducts:
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56 -algorithm:FeatureDeconvolution:potential_adducts
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57 #for token in $rep_param_algorithm_FeatureDeconvolution_potential_adducts:
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58 #if &quot; &quot; in str(token):
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59 &quot;$token.param_algorithm_FeatureDeconvolution_potential_adducts&quot;
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60 #else
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61 $token.param_algorithm_FeatureDeconvolution_potential_adducts
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62 #end if
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63 #end for
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64 #end if
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65 #if $param_algorithm_FeatureDeconvolution_max_neutrals:
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66 -algorithm:FeatureDeconvolution:max_neutrals $param_algorithm_FeatureDeconvolution_max_neutrals
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67 #end if
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68 #if $param_algorithm_FeatureDeconvolution_max_minority_bound:
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69 -algorithm:FeatureDeconvolution:max_minority_bound $param_algorithm_FeatureDeconvolution_max_minority_bound
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70 #end if
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71 #if $param_algorithm_FeatureDeconvolution_min_rt_overlap:
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72 -algorithm:FeatureDeconvolution:min_rt_overlap $param_algorithm_FeatureDeconvolution_min_rt_overlap
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73 #end if
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74 #if $param_algorithm_FeatureDeconvolution_intensity_filter:
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75 -algorithm:FeatureDeconvolution:intensity_filter
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76 #end if
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77 #if $adv_opts.adv_opts_selector=='advanced':
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78 #if $adv_opts.param_force:
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79 -force
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80 #end if
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81 #if $adv_opts.param_algorithm_FeatureDeconvolution_default_map_label:
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82 -algorithm:FeatureDeconvolution:default_map_label &quot;$adv_opts.param_algorithm_FeatureDeconvolution_default_map_label&quot;
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83 #end if
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84 #if $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level:
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85 -algorithm:FeatureDeconvolution:verbose_level $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level
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86 #end if
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87 #end if
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88 </command>
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89 <inputs>
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90 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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91 <param help="(-charge_min) " label="Minimal possible charge" name="param_algorithm_FeatureDeconvolution_charge_min" type="integer" value="1"/>
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92 <param help="(-charge_max) " label="Maximal possible charge" name="param_algorithm_FeatureDeconvolution_charge_max" type="integer" value="10"/>
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93 <param help="(-charge_span_max) observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge" label="Maximal range of charges for a single analyte, i.e" min="1" name="param_algorithm_FeatureDeconvolution_charge_span_max" optional="True" type="integer" value="4"/>
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94 <param help="(-q_try) " label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')" name="param_algorithm_FeatureDeconvolution_q_try" optional="True" type="select" value="feature">
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95 <option value="feature">feature</option>
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96 <option value="heuristic">heuristic</option>
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97 <option value="all">all</option>
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98 </param>
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99 <param help="(-retention_max_diff) " label="Maximum allowed RT difference between any two features if their relation shall be determined" name="param_algorithm_FeatureDeconvolution_retention_max_diff" type="float" value="1.0"/>
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100 <param help="(-retention_max_diff_local) " label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" name="param_algorithm_FeatureDeconvolution_retention_max_diff_local" type="float" value="1.0"/>
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101 <param help="(-mass_max_diff) " label="Maximum allowed mass difference [in Th] for a single feature" name="param_algorithm_FeatureDeconvolution_mass_max_diff" type="float" value="0.5"/>
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102 <repeat max="1" min="0" name="rep_param_algorithm_FeatureDeconvolution_potential_adducts" title="param_algorithm_FeatureDeconvolution_potential_adducts">
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103 <param help="(-potential_adducts) e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file" label="Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge," name="param_algorithm_FeatureDeconvolution_potential_adducts" size="30" type="text" value="H+:0.9">
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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="'"/>
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107 <remove value="&quot;"/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 </repeat>
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112 <param help="(-max_neutrals) Add them in the 'potential_adducts' section!" label="Maximal number of neutral adducts(q=0) allowed" name="param_algorithm_FeatureDeconvolution_max_neutrals" type="integer" value="0"/>
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113 <param help="(-max_minority_bound) E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct" label="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant" min="0" name="param_algorithm_FeatureDeconvolution_max_minority_bound" optional="True" type="integer" value="2"/>
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114 <param help="(-min_rt_overlap) " label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" max="1.0" min="0.0" name="param_algorithm_FeatureDeconvolution_min_rt_overlap" optional="True" type="float" value="0.66"/>
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115 <param checked="false" falsevalue="" help="(-intensity_filter) It is not used for features of different charge" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature" name="param_algorithm_FeatureDeconvolution_intensity_filter" optional="True" truevalue="-algorithm:FeatureDeconvolution:intensity_filter" type="boolean"/>
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116 <expand macro="advanced_options">
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117 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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118 <param help="(-default_map_label) " label="Label of map in output consensus file where all features are put by default" name="param_algorithm_FeatureDeconvolution_default_map_label" size="30" type="text" value="decharged features">
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119 <sanitizer>
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120 <valid initial="string.printable">
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121 <remove value="'"/>
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122 <remove value="&quot;"/>
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123 </valid>
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124 </sanitizer>
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125 </param>
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126 <param help="(-verbose_level) " label="Amount of debug information given during processing" max="3" min="0" name="param_algorithm_FeatureDeconvolution_verbose_level" optional="True" type="integer" value="0"/>
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127 </expand>
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128 </inputs>
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129 <outputs>
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130 <data format="consensusxml" name="param_out_cm"/>
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131 <data format="xml" name="param_out_fm"/>
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132 <data format="consensusxml" name="param_outpairs"/>
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133 </outputs>
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134 <help>Decharges and merges different feature charge variants of the same peptide.
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135
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136
4
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137 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html</help>
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138 </tool>