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annotate unipept.xml @ 3:bbfabdc0701c draft

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"planemo upload for repository http://unipept.ugent.be/apidocs commit 8df6ead5016e2c045a89ab2d0026a0c97d3cf8a1"
author galaxyp
date Mon, 01 Jun 2020 21:17:46 +0000
parents dca8a1fe0bf3
children 1137ffa5e479
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dca8a1fe0bf3 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6"
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1 <tool id="unipept" name="Unipept" version="4.3.0">
0
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2 <description>retrieve taxonomy for peptides</description>
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3 <macros>
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4 <xml name="equate_il">
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5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
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6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
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7 </param>
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8 </xml>
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9 <xml name="extra">
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10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
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11 <yield/>
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12 </param>
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13 </xml>
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14 <xml name="extra_true">
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15 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
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16 <yield/>
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17 </param>
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18 </xml>
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19 <xml name="names">
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20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
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21 <help>return the names in complete taxonomic lineage</help>
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22 </param>
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23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
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24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
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25 </param>
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26 </xml>
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27 <xml name="domains">
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28 <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">
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29 <yield/>
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30 </param>
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31 </xml>
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32 <xml name="selected_outputs">
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33 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
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34 <option value="tsv" selected="true">Tabular with one line per peptide</option>
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35 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
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36 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
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37 <yield/>
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38 <option value="unmatched">Unmatched peptides</option>
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39 </param>
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40 </xml>
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41 </macros>
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42 <requirements>
2
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43 <requirement type="package" version="3">python</requirement>
0
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44 </requirements>
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45 <stdio>
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46 <exit_code range="1:" />
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47 </stdio>
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48 <command><![CDATA[
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49 python '$__tool_directory__/unipept.py'
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50 ## --url 'http://morty.ugent.be/api/v1' -g -M 1
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51 --api=$unipept.api
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52 $unipept.equate_il $unipept.extra
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53 #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
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54 $unipept.names $unipept.allfields
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55 #end if
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56 #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
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57 $unipept.domains
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58 #end if
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59 $strict
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60 #if str($peptide_src.fmt) == 'proteomic':
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61 #if $peptide_src.input.datatype.file_ext == 'fasta':
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62 --fasta="$peptide_src.input"
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63 #elif $peptide_src.input.datatype.file_ext == 'mzid':
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64 --mzid="$peptide_src.input"
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65 #elif $peptide_src.input.datatype.file_ext == 'pepxml':
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66 --pepxml="$peptide_src.input"
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67 #end if
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68 #elif str($peptide_src.fmt) == 'tabular':
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69 --tabular="$peptide_src.input_tsv"
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70 #set $col = int(str($peptide_src.column)) - 1
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71 --column=$col
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72 #elif str($peptide_src.fmt) == 'fasta':
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73 --fasta="$peptide_src.input_fasta"
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74 #elif str($peptide_src.fmt) == 'mzid':
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75 --mzid="$peptide_src.input_mzid"
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76 #elif str($peptide_src.fmt) == 'pepxml':
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77 --pepxml="$peptide_src.input_pepxml"
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78 #end if
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79 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
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80 --json $output_json
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81 #end if
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82 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
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83 --ec_json $output_ec_json
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84 #end if
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85 #if 'tsv' in str($selected_outputs).split(','):
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86 --tsv $output_tsv
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87 #end if
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88 #if 'csv' in str($selected_outputs).split(','):
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89 --csv $output_csv
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90 #end if
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91 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
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92 --ec_tsv $output_ec_tsv
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93 #end if
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94 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
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95 --go_tsv $output_go_tsv
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96 #end if
2
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97 #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
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98 --ipr_tsv $output_ipr_tsv
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99 #end if
0
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100 #if 'unmatched' in str($selected_outputs).split(','):
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101 --unmatched $output_unmatched
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102 #end if
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103 ]]></command>
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104 <inputs>
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105 <conditional name="unipept">
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106 <param name="api" type="select" label="Unipept application" >
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107 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
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108 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
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109 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
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110 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
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111 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
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112 <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
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113 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
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114 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
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115 </param>
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116 <when value="pept2lca">
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117 <expand macro="equate_il" />
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118 <expand macro="extra">
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119 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
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120 </expand>
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121 <expand macro="names" />
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122 </when>
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123 <when value="pept2taxa">
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124 <expand macro="equate_il" />
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125 <expand macro="extra_true">
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126 <help>Return the complete lineage of each organism, and include ID fields.</help>
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127 </expand>
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128 <expand macro="names" />
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129 </when>
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130 <when value="pept2prot">
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131 <expand macro="equate_il" />
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132 <expand macro="extra">
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133 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
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134 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
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135 </help>
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136 </expand>
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137 </when>
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138 <when value="pept2ec">
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139 <expand macro="equate_il" />
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140 <expand macro="extra_true">
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141 <help>Return the name of the EC-number.
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142 </help>
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143 </expand>
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144 </when>
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145 <when value="pept2go">
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146 <expand macro="equate_il" />
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147 <expand macro="extra_true">
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148 <help>Return the name of the GO-term.
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149 </help>
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150 </expand>
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151 <expand macro="domains" />
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152 </when>
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153 <when value="pept2interpro">
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154 <expand macro="equate_il" />
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155 <expand macro="extra_true">
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156 <help>Return the name of the GO-term.
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157 </help>
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158 </expand>
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159 <expand macro="domains" />
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160 </when>
0
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161 <when value="pept2funct">
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162 <expand macro="equate_il" />
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163 <expand macro="extra_true">
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164 <help>Return the name of the EC-number and GO-term.
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165 </help>
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166 </expand>
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167 <expand macro="domains" />
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168 </when>
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169 <when value="peptinfo">
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170 <expand macro="equate_il" />
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171 <expand macro="extra_true">
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172 <help>Return the name of the EC-number and GO-term.
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173 </help>
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174 </expand>
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175 <expand macro="domains" />
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176 <expand macro="names" />
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177 </when>
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178 </conditional>
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179 <conditional name="peptide_src">
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180 <param name="fmt" type="select" label="Peptides input format" >
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181 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
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182 <option value="tabular">tabular</option>
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183 <option value="fasta">fasta</option>
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184 <option value="mzid">mzid</option>
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185 <option value="pepxml">pepxml</option>
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186 </param>
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187 <when value="proteomic">
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188 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
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189 </when>
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190 <when value="tabular">
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191 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
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192 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
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193 </when>
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194 <when value="fasta">
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195 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
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196 </when>
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197 <when value="mzid">
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198 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
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199 </when>
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200 <when value="pepxml">
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201 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
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202 </when>
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203 </conditional>
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204 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
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205 <option value="tsv" selected="true">Tabular with one line per peptide</option>
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206 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
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207 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
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208 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
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209 <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
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210 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
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211 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
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212 <option value="unmatched">Unmatched peptides</option>
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213 </param>
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214 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
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215 </inputs>
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216 <outputs>
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217 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
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218 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
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219 <change_format>
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220 <when input="api" value="pept2prot" format="json" />
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221 </change_format>
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222 </data>
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223 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
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224 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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225 </data>
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226 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
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227 <filter>'tsv' in selected_outputs</filter>
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228 <actions>
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229 <action name="comment_lines" type="metadata" default="1" />
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230 <!--
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231 <conditional name="unipept.api">
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232 <when value="pept2funct">
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233 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
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234 </when>
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235 <when value="pept2go">
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236 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
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237 </when>
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238 <when value="pept2ec">
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239 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
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240 </when>
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241 </conditional>
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242 -->
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243 </actions>
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244 </data>
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245 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
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246 <filter>'csv' in selected_outputs</filter>
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247 </data>
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248 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
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249 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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250 <actions>
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251 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
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252 </actions>
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253 </data>
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254 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
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255 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
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256 <actions>
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257 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
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258 </actions>
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259 </data>
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260 <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
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261 <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
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262 <actions>
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263 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
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264 </actions>
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265 </data>
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266
0
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267 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
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268 <filter>'unmatched' in selected_outputs</filter>
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269 <actions>
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270 <action name="column_names" type="metadata" default="Unmatched Peptide" />
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271 </actions>
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272 </data>
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273 </outputs>
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274 <tests>
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275 <test>
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276 <param name="api" value="pept2lca"/>
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277 <param name="fmt" value="tabular"/>
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278 <param name="input_tsv" value="tryptic.tsv"/>
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279 <param name="column" value="2"/>
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280 <param name="extra" value="True"/>
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281 <param name="names" value="True"/>
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282 <param name="selected_outputs" value="tsv,unmatched"/>
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283 <output name="output_tsv">
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284 <assert_contents>
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285 <has_text text="Homininae" />
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286 </assert_contents>
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287 </output>
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288 <output name="output_unmatched">
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289 <assert_contents>
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290 <has_text text="QTAMAV" />
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291 </assert_contents>
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292 </output>
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293 </test>
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294 <test>
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295 <param name="api" value="pept2lca"/>
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296 <param name="fmt" value="fasta"/>
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297 <param name="input_fasta" value="peptide.fa"/>
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298 <param name="equate_il" value="True"/>
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299 <param name="extra" value="True"/>
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300 <param name="names" value="True"/>
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301 <param name="selected_outputs" value="json,tsv"/>
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302 <!--
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303 -->
0
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304 <output name="output_json">
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305 <assert_contents>
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306 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
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307 </assert_contents>
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308 </output>
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309 <output name="output_tsv">
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310 <assert_contents>
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311 <has_text text="9606" />
1
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312 <has_text text="9596" />
0
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313 </assert_contents>
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314 </output>
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315 </test>
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316 <test>
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317 <param name="api" value="pept2taxa"/>
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318 <param name="fmt" value="fasta"/>
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319 <param name="input_fasta" value="peptide.fa"/>
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320 <param name="equate_il" value="True"/>
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321 <param name="extra" value="False"/>
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322 <param name="names" value="False"/>
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323 <param name="selected_outputs" value="tsv"/>
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324 <output name="output_tsv">
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325 <assert_contents>
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326 <has_text text="sapiens" />
1
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327 <has_text text="paniscus" />
0
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328 </assert_contents>
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329 </output>
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330 </test>
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331 <test>
1
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332 <param name="api" value="pept2funct"/>
0
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333 <param name="fmt" value="tabular"/>
1
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334 <param name="input_tsv" value="input.tsv"/>
0
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335 <param name="column" value="2"/>
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336 <param name="extra" value="True"/>
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337 <param name="names" value="True"/>
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338 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
0
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339 <output name="output_tsv">
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340 <assert_contents>
1
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341 <has_text text="GO:0004802" />
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342 <has_text text="2.2.1.1" />
2
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343 <has_text text="IPR005475" />
0
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344 </assert_contents>
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345 </output>
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346 <output name="output_ec_tsv">
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347 <assert_contents>
1
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348 <has_text text="2.2.1.1" />
0
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349 </assert_contents>
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350 </output>
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351 <output name="output_go_tsv">
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352 <assert_contents>
1
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353 <has_text text="GO:0004802" />
0
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354 </assert_contents>
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355 </output>
2
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356 <output name="output_ipr_tsv">
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357 <assert_contents>
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358 <has_text text="IPR005475" />
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359 </assert_contents>
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360 </output>
0
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361 </test>
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362 </tests>
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363 <help><![CDATA[
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364 **Unipept**
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365
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366 Retrieve Uniprot and taxanomic information for trypic peptides.
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367
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368 Unipept API documentation - http://unipept.ugent.be/apidocs
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369
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370 **Input**
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371
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372 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
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373
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374 Processing deatils::
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375
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376 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
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377 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
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378 The match to the most specific tryptic fragment is reported.
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379
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380
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381 **Unipept APIs**
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382
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383 **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot
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384
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385 Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface.
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386
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387 By default, each object contains the following information fields extracted from the UniProt record::
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388
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389 peptide: the peptide that matched this record
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390 uniprot_id: the UniProt accession number of the matching record
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391 taxon_id: the NCBI taxon id of the organism associated with the matching record
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392
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393 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
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394
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395 taxon_name: the name of the organism associated with the matching UniProt record
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396 ec_references: a space separated list of associated EC numbers
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397 go_references: a space separated list of associated GO terms
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398 refseq_ids: a space separated list of associated RefSeq accession numbers
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399 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
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400 insdc_ids: a space separated list of associated insdc accession numbers
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401 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
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402
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403
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404 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa
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405
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406 Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface.
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407
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408 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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409
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410 peptide: the peptide that matched this record
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411 taxon_id: the NCBI taxon id of the organism associated with the matching record
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412 taxon_name: the name of the organism associated with the matching record
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413 taxon_rank: the taxonomic rank of the organism associated with the matching record
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414
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415 When the extra parameter is set to true, objects contain additional information about the lineages of the organism extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
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416
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417 superkingdom_id
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418 kingdom_id
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419 subkingdom_id
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420 superphylum_id
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421 phylum_id
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422 subphylum_id
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423 superclass_id
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424 class_id
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425 subclass_id
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426 infraclass_id
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427 superorder_id
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428 order_id
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429 suborder_id
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430 infraorder_id
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431 parvorder_id
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432 superfamily_id
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433 family_id
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434 subfamily_id
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435 tribe_id
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436 subtribe_id
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437 genus_id
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438 subgenus_id
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439 species_group_id
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440 species_subgroup_id
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441 species_id
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442 subspecies_id
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443 varietas_id
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444 forma_id
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445
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446
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447 **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca
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448
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449 Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
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450
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451 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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452
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453 peptide: the peptide that matched this record
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454 taxon_id: the NCBI taxon id of the organism associated with the matching record
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455 taxon_name: the name of the organism associated with the matching record
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456 taxon_rank: the taxonomic rank of the organism associated with the matching record
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457
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458 When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
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459
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460 superkingdom_id
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461 kingdom_id
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462 subkingdom_id
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463 superphylum_id
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464 phylum_id
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465 subphylum_id
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466 superclass_id
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467 class_id
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468 subclass_id
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469 infraclass_id
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470 superorder_id
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471 order_id
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472 suborder_id
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473 infraorder_id
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474 parvorder_id
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475 superfamily_id
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476 family_id
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477 subfamily_id
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478 tribe_id
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479 subtribe_id
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480 genus_id
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481 subgenus_id
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482 species_group_id
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483 species_subgroup_id
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484 species_id
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485 subspecies_id
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486 varietas_id
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487 forma_id
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488
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489 **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec
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490
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491 Returns the functional EC-numbers associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
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492
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493 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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494
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495 peptide: the peptide that matched this record
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496 total_protein_count: Total amount of proteins matched with the given peptide
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497 ec_number: EC-number associated with the current tryptic peptide.
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498 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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499 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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500
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501
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502 **pept2go** - http://unipept.ugent.be/apidocs/pept2go
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503
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504 Returns the functional GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
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505
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506 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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507
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508 peptide: the peptide that matched this record
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509 total_protein_count: Total amount of proteins matched with the given peptide
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510 go_term: The GO-term associated with the current tryptic peptide.
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511 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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512 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
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513
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514
2
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515 **pept2interpro** - http://unipept.ugent.be/apidocs/pept2interpro
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516
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517 Returns the functional InterPro entries associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
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518
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519 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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520
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521 peptide: the peptide that matched this record
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522 total_protein_count: Total amount of proteins matched with the given peptide
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523 code: InterPro entry code associated with the current tryptic peptide
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524 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
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525 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
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526 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
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527
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528 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct
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529
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530 Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
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531
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532 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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533
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534 peptide: the peptide that matched this record
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535 total_protein_count: Total amount of proteins matched with the given peptide
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536 ec_number: EC-number associated with the current tryptic peptide.
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537 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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538 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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539 go_term: The GO-term associated with the current tryptic peptide.
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540 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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541 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
2
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542 code: InterPro entry code associated with the current tryptic peptide
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543 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
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544 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
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545 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
0
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546
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547
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548 **Attributions**
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549
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550 The Unipept metaproteomics analysis pipeline
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551 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
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552 Article first published online: 11 FEB 2015
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553 DOI: 10.1002/pmic.201400361
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554 http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04
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555
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556 ]]></help>
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557 <citations>
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558 <citation type="doi">doi:10.1002/pmic.201400361</citation>
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559 </citations>
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560
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561 </tool>