annotate PeptideIndexer.xml @ 8:5182338d5e7c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:07:01 -0400
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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: [ID Processing]-->
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4 <tool id="PeptideIndexer" name="PeptideIndexer" version="2.3.0">
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5 <description>Refreshes the protein references for all peptide hits.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PeptideIndexer</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 detect_errors="aggressive"><![CDATA[PeptideIndexer
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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_fasta:
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19 -fasta $param_fasta
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_decoy_string:
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25 -decoy_string "$param_decoy_string"
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26 #end if
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27 #if $param_decoy_string_position:
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28 -decoy_string_position
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29 #if " " in str($param_decoy_string_position):
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30 "$param_decoy_string_position"
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31 #else
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32 $param_decoy_string_position
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33 #end if
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34 #end if
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35 #if $param_missing_decoy_action:
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36 -missing_decoy_action
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37 #if " " in str($param_missing_decoy_action):
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38 "$param_missing_decoy_action"
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39 #else
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40 $param_missing_decoy_action
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41 #end if
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42 #end if
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43 #if $param_write_protein_sequence:
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44 -write_protein_sequence
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45 #end if
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46 #if $param_write_protein_description:
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47 -write_protein_description
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48 #end if
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49 #if $param_keep_unreferenced_proteins:
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50 -keep_unreferenced_proteins
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51 #end if
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52 #if $param_allow_unmatched:
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53 -allow_unmatched
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54 #end if
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55 #if $param_full_tolerant_search:
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56 -full_tolerant_search
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57 #end if
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58 #if $param_aaa_max:
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59 -aaa_max $param_aaa_max
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60 #end if
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61 #if $param_mismatches_max:
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62 -mismatches_max $param_mismatches_max
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63 #end if
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64 #if $param_IL_equivalent:
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65 -IL_equivalent
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66 #end if
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67 #if $param_filter_aaa_proteins:
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68 -filter_aaa_proteins
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69 #end if
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70 #if $param_enzyme_name:
1
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71 -enzyme:name
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72 #if " " in str($param_enzyme_name):
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73 "$param_enzyme_name"
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74 #else
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75 $param_enzyme_name
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76 #end if
0
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77 #end if
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78 #if $param_enzyme_specificity:
1
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79 -enzyme:specificity
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80 #if " " in str($param_enzyme_specificity):
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81 "$param_enzyme_specificity"
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82 #else
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83 $param_enzyme_specificity
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84 #end if
0
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85 #end if
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86 #if $adv_opts.adv_opts_selector=='advanced':
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87 #if $adv_opts.param_force:
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88 -force
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89 #end if
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90 #end if
7
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91 -threads "\${GALAXY_SLOTS:-1}"
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92 ]]></command>
0
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93 <inputs>
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94 <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
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95 <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
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96 <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
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97 <sanitizer>
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98 <valid initial="string.printable">
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99 <remove value="'"/>
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100 <remove value="&quot;"/>
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101 </valid>
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102 </sanitizer>
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103 </param>
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104 <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
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105 <option value="prefix" selected="true">prefix</option>
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106 <option value="suffix">suffix</option>
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107 </param>
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108 <param name="param_missing_decoy_action" display="radio" type="select" optional="False" value="error" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)" help="(-missing_decoy_action) ">
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109 <option value="error" selected="true">error</option>
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110 <option value="warn">warn</option>
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111 </param>
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112 <param name="param_write_protein_sequence" display="radio" type="boolean" truevalue="-write_protein_sequence" falsevalue="" checked="false" optional="True" label="If set, the protein sequences are stored as well" help="(-write_protein_sequence) "/>
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113 <param name="param_write_protein_description" display="radio" type="boolean" truevalue="-write_protein_description" falsevalue="" checked="false" optional="True" label="If set, the protein description is stored as well" help="(-write_protein_description) "/>
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114 <param name="param_keep_unreferenced_proteins" display="radio" type="boolean" truevalue="-keep_unreferenced_proteins" falsevalue="" checked="false" optional="True" label="If set, protein hits which are not referenced by any peptide are kept" help="(-keep_unreferenced_proteins) "/>
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115 <param name="param_allow_unmatched" display="radio" type="boolean" truevalue="-allow_unmatched" falsevalue="" checked="false" optional="True" label="If set, unmatched peptide sequences are allowed" help="(-allow_unmatched) By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/>
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116 <param name="param_full_tolerant_search" display="radio" type="boolean" truevalue="-full_tolerant_search" falsevalue="" checked="false" optional="True" label="If set, all peptide sequences are matched using tolerant search" help="(-full_tolerant_search) Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!"/>
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117 <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="[tolerant search only] Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="(-aaa_max) AAAs are 'B', 'Z' and 'X'"/>
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118 <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/>
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119 <param name="param_IL_equivalent" display="radio" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
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120 <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
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121 <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
1
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122 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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123 <option value="TrypChymo">TrypChymo</option>
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124 <option value="unspecific cleavage">unspecific cleavage</option>
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125 <option value="Trypsin/P">Trypsin/P</option>
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126 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
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127 <option value="V8-DE">V8-DE</option>
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128 <option value="V8-E">V8-E</option>
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129 <option value="PepsinA">PepsinA</option>
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130 <option value="Asp-N">Asp-N</option>
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131 <option value="2-iodobenzoate">2-iodobenzoate</option>
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132 <option value="Lys-N">Lys-N</option>
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133 <option value="Asp-N_ambic">Asp-N_ambic</option>
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134 <option value="CNBr">CNBr</option>
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135 <option value="Asp-N/B">Asp-N/B</option>
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136 <option value="Formic_acid">Formic_acid</option>
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137 <option value="Chymotrypsin">Chymotrypsin</option>
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138 <option value="Lys-C">Lys-C</option>
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139 <option value="Trypsin" selected="true">Trypsin</option>
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140 <option value="Arg-C">Arg-C</option>
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141 <option value="Arg-C/P">Arg-C/P</option>
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142 <option value="Lys-C/P">Lys-C/P</option>
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143 <option value="no cleavage">no cleavage</option>
0
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144 <option value="leukocyte elastase">leukocyte elastase</option>
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145 <option value="proline endopeptidase">proline endopeptidase</option>
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146 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
0
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147 </param>
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148 <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt; 'full': both internal cleavage sites must match. &lt;br&gt; 'semi': one of two internal cleavage sites must match. &lt;br&gt; 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
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149 <option value="full" selected="true">full</option>
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150 <option value="semi">semi</option>
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151 <option value="none">none</option>
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152 </param>
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153 <expand macro="advanced_options">
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154 <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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155 </expand>
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156 </inputs>
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157 <outputs>
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158 <data name="param_out" format="idxml"/>
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159 </outputs>
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160 <help>Refreshes the protein references for all peptide hits.
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161
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162
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163 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeptideIndexer.html</help>
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164 </tool>