Mercurial > repos > galaxyp > peptideshaker

annotate macros.xml @ 45:5fa8b409599e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
author galaxyp
date Mon, 30 Apr 2018 04:41:50 -0400
parents 7963340ab569
children baeced706dbc
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Job Failed" />
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5 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
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8 </stdio>
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9 </xml>
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10 <token name="@GENERAL_PARAMETERS@">
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11 -frag_tol '${precursor_options.fragment_tol}'
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12 -frag_ppm '${precursor_options.fragment_tol_units}'
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13 -prec_tol '${precursor_options.precursor_ion_tol}'
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14 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
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16 -min_charge $precursor_options.min_charge
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17 -max_charge $precursor_options.max_charge
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18 -fi $precursor_options.forward_ion
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19 -ri $precursor_options.reverse_ion
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20 -min_isotope ${precursor_options.min_isotope}
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21 -max_isotope ${precursor_options.max_isotope}
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22 #if $protein_digest_options.digestion.cleavage == 'default':
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23 ## -enzyme "Trysin"
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24 -mc $protein_digest_options.digestion.missed_cleavages
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25 #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
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26 #set $enzymes = []
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27 #set $missed_cleavages = []
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28 ## #set $specificities = []
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29 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
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30 #silent $enzymes.append(str($digest.enzyme))
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31 #silent $missed_cleavages.append(str($digest.missed_cleavages))
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32 ## #silent $specificities.append(str($digest.specificity))
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33 #end for
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34 -enzyme "#echo ','.join($enzymes)#"
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35 -mc "#echo ','.join($missed_cleavages)#"
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36 ## -specificity "#echo ','.join($specificities)#"
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37 #else:
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38 -digestion $protein_digest_options.digestion.cleavage
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39 #end if
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41 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
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42 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
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43 #if $fixed_mods_str
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44 -fixed_mods "$fixed_mods_str"
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45 #end if
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46 #if $variable_mods_str
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47 -variable_mods "$variable_mods_str"
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48 #end if
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49
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50 </token>
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51 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
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52 <token name="@SEARCHGUI_VERSION@">3.2.24</token>
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53 <xml name="general_options">
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54
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55 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
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56 <conditional name="digestion">
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57 <param name="cleavage" type="select" label="Digestion">
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58 <option value="default" selected="true">Trypsin</option>
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59 <option value="0">Select Enzymes</option>
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60 <option value="1">Unspecific Cleavage</option>
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61 <option value="2">Whole Protein</option>
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62 </param>
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63 <when value="default">
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64 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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65 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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66 </when>
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67 <when value="0">
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68 <repeat name="digests" min="1" title="Enzymes">
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69 <param name="enzyme" type="select" label="Enzyme"
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70 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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71 <option value="Trypsin">Trypsin</option>
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72 <option value="Arg-C">Arg-C</option>
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73 <option value="CNBr">CNBr</option>
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74 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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75 <option value="Formic Acid">Formic Acid</option>
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76 <option value="Lys-C">Lys-C</option>
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77 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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78 <option value="Pepsin A">Pepsin A</option>
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79 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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80 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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81 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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82 <option value="Whole Protein">Whole Protein</option>
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83 <option value="Asp-N">Asp-N</option>
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84 <option value="Glu-C">Glu-C</option>
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85 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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86 <option value="Top-Down">Top-Down</option>
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87 <option value="Semi-Tryptic">Semi-Tryptic</option>
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88 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
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89 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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90 <option value="Asp-N (DE)">Asp-N (DE)</option>
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91 <option value="Glu-C (DE)">Glu-C (DE)</option>
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92 <option value="Lys-N (K)">Lys-N (K)</option>
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93 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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94 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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95 <option value="Semi-Glu-C">Semi-Glu-C</option>
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96 <option value="LysargiNase">LysargiNase</option>
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97 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
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98 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
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99 <option value="Semi-Arg-C">Semi-Arg-C</option>
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100 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
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101 <option value="Arg-N">Arg-N</option>
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102 <option value="Semi-Arg-N">Semi-Arg-N</option>
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103 </param>
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104 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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105 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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106 <!--
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107 <param name="specificity" type="select" label="Specificity">
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108 <option value="0" selected="true">Specific at both termini</option>
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109 <option value="1">Semi-Specific - one terminus</option>
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110 <option value="2">Specific at the N-terminus only</option>
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111 <option value="3">Specific at the C-terminus only</option>
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112 </param>
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113 -->
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114 </repeat>
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115 </when>
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116 <when value="1"/>
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117 <when value="2"/>
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118 </conditional>
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119 </section>
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120
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121 <section name="precursor_options" expanded="false" title="Precursor Options">
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122 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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123 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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124 <option value="1">Parts per million (ppm)</option>
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125 <option value="0">Daltons</option>
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126 </param>
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127 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
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128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
41
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129 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
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130 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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131 <option value="1">Parts per million (ppm)</option>
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132 <option value="0" selected="true">Daltons</option>
41
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133 </param>
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134 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
33
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135 help="Provide error value for fragment ions, based on instrument used"/>
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136 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
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137 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
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138 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
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139 <option value="a">a</option>
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140 <option value="b" selected="true">b</option>
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141 <option value="c">c</option>
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142 </param>
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143 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
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144 <option value="x">x</option>
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145 <option value="y" selected="true">y</option>
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146 <option value="z">z</option>
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147 </param>
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148 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
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149 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
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150 </section>
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151
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152 <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
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153 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
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154 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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155 <options from_file="searchgui_mods.loc">
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156 <column name="name" index="0" />
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157 <column name="value" index="0" />
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158 </options>
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159 </param>
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160 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
33
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161 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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162 <options from_file="searchgui_mods.loc">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
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163 <column name="name" index="0" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
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164 <column name="value" index="0" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
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165 </options>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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166 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
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167 </section>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
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168
20
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iracooke
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169 </xml>
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170
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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171 <xml name="citations">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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172 <citations>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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173 <citation type="doi">10.1186/1471-2105-12-70</citation>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
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174 <citation type="doi">10.1002/pmic.201000595</citation>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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175 <citation type="doi">doi:10.1038/nbt.3109</citation>
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iracooke
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176 </citations>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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177 </xml>
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178
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iracooke
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179 </macros>