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annotate unipept.xml @ 5:42bc03ed02f6 draft default tip

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planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
author galaxyp
date Sat, 02 Jul 2022 13:46:02 +0000
parents 1137ffa5e479
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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42bc03ed02f6 planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
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1 <tool id="unipept" name="Unipept" version="4.5.1">
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
4
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79 --peptide_match $peptide_match
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80 #if $peptide_match == 'report' and $unmatched_aa != 'default':
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81 --unmatched_aa $unmatched_aa
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82 #end if
0
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83 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
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84 --json $output_json
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85 #end if
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86 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
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87 --ec_json $output_ec_json
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88 #end if
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89 #if 'tsv' in str($selected_outputs).split(','):
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90 --tsv $output_tsv
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91 #end if
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92 #if 'csv' in str($selected_outputs).split(','):
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93 --csv $output_csv
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94 #end if
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95 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
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96 --ec_tsv $output_ec_tsv
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97 #end if
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98 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
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99 --go_tsv $output_go_tsv
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100 #end if
2
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101 #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
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102 --ipr_tsv $output_ipr_tsv
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103 #end if
0
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104 #if 'unmatched' in str($selected_outputs).split(','):
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105 --unmatched $output_unmatched
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106 #end if
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107 ]]></command>
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108 <inputs>
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109 <conditional name="unipept">
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110 <param name="api" type="select" label="Unipept application" >
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111 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
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112 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
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113 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
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114 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
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115 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
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116 <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
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117 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
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118 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
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119 </param>
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120 <when value="pept2lca">
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121 <expand macro="equate_il" />
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122 <expand macro="extra">
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123 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
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124 </expand>
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125 <expand macro="names" />
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126 </when>
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127 <when value="pept2taxa">
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128 <expand macro="equate_il" />
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129 <expand macro="extra_true">
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130 <help>Return the complete lineage of each organism, and include ID fields.</help>
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131 </expand>
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132 <expand macro="names" />
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133 </when>
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134 <when value="pept2prot">
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135 <expand macro="equate_il" />
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136 <expand macro="extra">
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137 <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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138 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
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139 </help>
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140 </expand>
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141 </when>
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142 <when value="pept2ec">
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143 <expand macro="equate_il" />
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144 <expand macro="extra_true">
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145 <help>Return the name of the EC-number.
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146 </help>
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147 </expand>
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148 </when>
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149 <when value="pept2go">
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150 <expand macro="equate_il" />
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151 <expand macro="extra_true">
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152 <help>Return the name of the GO-term.
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153 </help>
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154 </expand>
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155 <expand macro="domains" />
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156 </when>
2
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157 <when value="pept2interpro">
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158 <expand macro="equate_il" />
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159 <expand macro="extra_true">
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160 <help>Return the name of the GO-term.
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161 </help>
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162 </expand>
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163 <expand macro="domains" />
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164 </when>
0
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165 <when value="pept2funct">
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166 <expand macro="equate_il" />
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167 <expand macro="extra_true">
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168 <help>Return the name of the EC-number and GO-term.
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169 </help>
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170 </expand>
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171 <expand macro="domains" />
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172 </when>
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173 <when value="peptinfo">
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174 <expand macro="equate_il" />
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175 <expand macro="extra_true">
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176 <help>Return the name of the EC-number and GO-term.
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177 </help>
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178 </expand>
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179 <expand macro="domains" />
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180 <expand macro="names" />
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181 </when>
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182 </conditional>
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183 <conditional name="peptide_src">
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184 <param name="fmt" type="select" label="Peptides input format" >
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185 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
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186 <option value="tabular">tabular</option>
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187 <option value="fasta">fasta</option>
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188 <option value="mzid">mzid</option>
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189 <option value="pepxml">pepxml</option>
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190 </param>
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191 <when value="proteomic">
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192 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
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193 </when>
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194 <when value="tabular">
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195 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
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196 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
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197 </when>
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198 <when value="fasta">
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199 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
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200 </when>
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201 <when value="mzid">
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202 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
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203 </when>
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204 <when value="pepxml">
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205 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
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206 </when>
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207 </conditional>
4
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208 <param name="peptide_match" type="select" label="Match input peptides by">
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209 <option value="full">Match to the full input peptide</option>
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210 <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
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211 <option value="report">Best match to tryptic parts, add tryptic_match column</option>
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212 </param>
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213 <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
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214 <option value="default">List of matched tryptic parts</option>
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215 <option value=".">peptide with unmatched AAs as .</option>
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216 <option value="x">peptide with unmatched AAs as x</option>
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217 </param>
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218 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
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219 <option value="tsv" selected="true">Tabular with one line per peptide</option>
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220 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
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221 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
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222 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
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223 <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
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224 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
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225 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
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226 <option value="unmatched">Unmatched peptides</option>
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227 </param>
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228 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
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229 </inputs>
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230 <outputs>
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231 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
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232 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
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233 <change_format>
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234 <when input="api" value="pept2prot" format="json" />
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235 </change_format>
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236 </data>
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237 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
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238 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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239 </data>
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240 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
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241 <filter>'tsv' in selected_outputs</filter>
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242 <actions>
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243 <action name="comment_lines" type="metadata" default="1" />
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244 <!--
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245 <conditional name="unipept.api">
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246 <when value="pept2funct">
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247 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
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248 </when>
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249 <when value="pept2go">
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250 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
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251 </when>
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252 <when value="pept2ec">
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253 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
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254 </when>
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255 </conditional>
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256 -->
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257 </actions>
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258 </data>
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259 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
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260 <filter>'csv' in selected_outputs</filter>
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261 </data>
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262 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
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263 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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264 <actions>
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265 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
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266 </actions>
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267 </data>
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268 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
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269 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
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270 <actions>
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271 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
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272 </actions>
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273 </data>
2
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274 <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
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275 <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
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276 <actions>
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277 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
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278 </actions>
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279 </data>
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280
0
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281 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
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282 <filter>'unmatched' in selected_outputs</filter>
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283 <actions>
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284 <action name="column_names" type="metadata" default="Unmatched Peptide" />
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285 </actions>
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286 </data>
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287 </outputs>
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288 <tests>
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289 <!-- Test-1 -->
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290 <test>
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291 <param name="api" value="pept2lca"/>
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292 <param name="fmt" value="tabular"/>
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293 <param name="input_tsv" value="tryptic.tsv"/>
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294 <param name="column" value="2"/>
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295 <param name="extra" value="True"/>
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296 <param name="names" value="True"/>
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297 <param name="selected_outputs" value="tsv,unmatched"/>
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298 <output name="output_tsv">
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299 <assert_contents>
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300 <has_text text="Homininae" />
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301 </assert_contents>
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302 </output>
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303 <output name="output_unmatched">
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304 <assert_contents>
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305 <has_text text="QTAMAV" />
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306 </assert_contents>
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307 </output>
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308 </test>
4
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309 <!-- Test-2 -->
0
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310 <test>
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311 <param name="api" value="pept2lca"/>
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312 <param name="fmt" value="fasta"/>
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313 <param name="input_fasta" value="peptide.fa"/>
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314 <param name="equate_il" value="True"/>
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315 <param name="extra" value="True"/>
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316 <param name="names" value="True"/>
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317 <param name="selected_outputs" value="json,tsv"/>
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318 <output name="output_json">
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319 <assert_contents>
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320 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
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321 </assert_contents>
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322 </output>
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323 <output name="output_tsv">
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324 <assert_contents>
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325 <has_text text="9606" />
1
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326 <has_text text="9596" />
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327 </assert_contents>
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328 </output>
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329 </test>
4
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330 <!-- Test-3 -->
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331 <test>
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332 <param name="api" value="pept2taxa"/>
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333 <param name="fmt" value="fasta"/>
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334 <param name="input_fasta" value="peptide.fa"/>
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335 <param name="equate_il" value="True"/>
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336 <param name="extra" value="False"/>
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337 <param name="names" value="False"/>
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338 <param name="selected_outputs" value="tsv"/>
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339 <output name="output_tsv">
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340 <assert_contents>
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341 <has_text text="sapiens" />
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342 <has_text text="troglodytes" />
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343 </assert_contents>
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344 </output>
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345 </test>
4
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346 <!-- Test-4 -->
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347 <test>
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348 <param name="api" value="pept2funct"/>
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349 <param name="fmt" value="tabular"/>
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350 <param name="input_tsv" value="input.tsv"/>
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351 <param name="column" value="2"/>
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352 <param name="extra" value="True"/>
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353 <param name="names" value="True"/>
2
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354 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
0
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355 <output name="output_tsv">
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356 <assert_contents>
1
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357 <has_text text="GO:0004802" />
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358 <has_text text="2.2.1.1" />
2
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359 <has_text text="IPR005475" />
0
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360 </assert_contents>
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361 </output>
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362 <output name="output_ec_tsv">
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363 <assert_contents>
1
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364 <has_text text="2.2.1.1" />
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365 </assert_contents>
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366 </output>
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367 <output name="output_go_tsv">
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368 <assert_contents>
1
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369 <has_text text="GO:0004802" />
0
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370 </assert_contents>
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371 </output>
2
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372 <output name="output_ipr_tsv">
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373 <assert_contents>
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374 <has_text text="IPR005475" />
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375 </assert_contents>
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376 </output>
0
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377 </test>
4
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378 <!-- Test-5 -->
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379 <test>
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380 <param name="api" value="pept2funct"/>
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381 <param name="fmt" value="tabular"/>
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382 <param name="input_tsv" value="input.tsv"/>
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383 <param name="column" value="2"/>
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384 <param name="extra" value="True"/>
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385 <param name="names" value="True"/>
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386 <param name="peptide_match" value="full"/>
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387 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
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388 <output name="output_tsv">
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389 <assert_contents>
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390 <has_text text="GO:0004802" />
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391 <has_text text="2.2.1.1" />
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392 <has_text text="IPR005475" />
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393 <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" />
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394 </assert_contents>
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395 </output>
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396 <output name="output_ec_tsv">
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397 <assert_contents>
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398 <has_text text="2.2.1.1" />
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399 </assert_contents>
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400 </output>
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401 <output name="output_go_tsv">
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402 <assert_contents>
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403 <has_text text="GO:0004802" />
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404 </assert_contents>
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405 </output>
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406 <output name="output_ipr_tsv">
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407 <assert_contents>
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408 <has_text text="IPR005475" />
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409 </assert_contents>
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410 </output>
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411 </test>
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412 <!-- Test-6 -->
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413 <test>
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414 <param name="api" value="pept2funct"/>
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415 <param name="fmt" value="tabular"/>
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416 <param name="input_tsv" value="input.tsv"/>
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417 <param name="column" value="2"/>
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418 <param name="extra" value="True"/>
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419 <param name="names" value="True"/>
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420 <param name="peptide_match" value="report"/>
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421 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
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422 <output name="output_tsv">
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423 <assert_contents>
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424 <has_text text="GO:0004802" />
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425 <has_text text="2.2.1.1" />
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426 <has_text text="IPR005475" />
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427 <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" />
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428 </assert_contents>
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429 </output>
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430 <output name="output_ec_tsv">
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431 <assert_contents>
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432 <has_text text="2.2.1.1" />
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433 </assert_contents>
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434 </output>
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435 <output name="output_go_tsv">
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436 <assert_contents>
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437 <has_text text="GO:0004802" />
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438 </assert_contents>
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439 </output>
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440 <output name="output_ipr_tsv">
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441 <assert_contents>
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442 <has_text text="IPR005475" />
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443 </assert_contents>
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444 </output>
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445 </test>
0
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446 </tests>
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447 <help><![CDATA[
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448 **Unipept**
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449
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450 Retrieve Uniprot and taxanomic information for trypic peptides.
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451
5
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452 Unipept API documentation - https://unipept.ugent.be/apidocs
0
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453
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454 **Input**
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455
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456 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
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457
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458 Processing deatils::
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459
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460 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
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461 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
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462 The match to the most specific tryptic fragment is reported.
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463
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464
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465 **Unipept APIs**
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466
5
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467 **pept2prot** - https://unipept.ugent.be/apidocs/pept2prot
0
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468
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469 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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470
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471 By default, each object contains the following information fields extracted from the UniProt record::
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472
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473 peptide: the peptide that matched this record
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474 uniprot_id: the UniProt accession number of the matching record
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475 taxon_id: the NCBI taxon id of the organism associated with the matching record
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476
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477 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
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478
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479 taxon_name: the name of the organism associated with the matching UniProt record
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480 ec_references: a space separated list of associated EC numbers
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481 go_references: a space separated list of associated GO terms
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482 refseq_ids: a space separated list of associated RefSeq accession numbers
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483 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
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484 insdc_ids: a space separated list of associated insdc accession numbers
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485 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
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486
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487
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488 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa
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489
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490 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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491
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492 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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493
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494 peptide: the peptide that matched this record
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495 taxon_id: the NCBI taxon id of the organism associated with the matching record
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496 taxon_name: the name of the organism associated with the matching record
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497 taxon_rank: the taxonomic rank of the organism associated with the matching record
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498
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499 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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500
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501 superkingdom_id
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502 kingdom_id
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503 subkingdom_id
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504 superphylum_id
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505 phylum_id
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506 subphylum_id
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507 superclass_id
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508 class_id
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509 subclass_id
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510 infraclass_id
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511 superorder_id
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512 order_id
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513 suborder_id
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514 infraorder_id
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515 parvorder_id
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516 superfamily_id
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517 family_id
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518 subfamily_id
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519 tribe_id
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520 subtribe_id
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521 genus_id
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522 subgenus_id
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523 species_group_id
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524 species_subgroup_id
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525 species_id
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526 subspecies_id
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527 varietas_id
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528 forma_id
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529
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530
5
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diff changeset
531 **pept2lca** - https://unipept.ugent.be/apidocs/pept2lca
0
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532
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533 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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534
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535 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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536
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537 peptide: the peptide that matched this record
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538 taxon_id: the NCBI taxon id of the organism associated with the matching record
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539 taxon_name: the name of the organism associated with the matching record
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540 taxon_rank: the taxonomic rank of the organism associated with the matching record
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541
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542 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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543
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544 superkingdom_id
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545 kingdom_id
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546 subkingdom_id
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547 superphylum_id
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548 phylum_id
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549 subphylum_id
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550 superclass_id
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551 class_id
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552 subclass_id
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553 infraclass_id
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554 superorder_id
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555 order_id
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556 suborder_id
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557 infraorder_id
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558 parvorder_id
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559 superfamily_id
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560 family_id
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561 subfamily_id
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562 tribe_id
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563 subtribe_id
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564 genus_id
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565 subgenus_id
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566 species_group_id
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567 species_subgroup_id
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568 species_id
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569 subspecies_id
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570 varietas_id
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571 forma_id
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572
5
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diff changeset
573 **pept2ec** - https://unipept.ugent.be/apidocs/pept2ec
0
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574
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575 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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576
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577 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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578
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579 peptide: the peptide that matched this record
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580 total_protein_count: Total amount of proteins matched with the given peptide
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581 ec_number: EC-number associated with the current tryptic peptide.
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582 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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583 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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584
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585
5
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diff changeset
586 **pept2go** - https://unipept.ugent.be/apidocs/pept2go
0
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587
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588 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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589
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590 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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591
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592 peptide: the peptide that matched this record
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593 total_protein_count: Total amount of proteins matched with the given peptide
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594 go_term: The GO-term associated with the current tryptic peptide.
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595 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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596 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
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597
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598
5
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diff changeset
599 **pept2interpro** - https://unipept.ugent.be/apidocs/pept2interpro
2
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600
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601 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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602
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603 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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604
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diff changeset
605 peptide: the peptide that matched this record
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606 total_protein_count: Total amount of proteins matched with the given peptide
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607 code: InterPro entry code associated with the current tryptic peptide
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608 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
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609 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
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610 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
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611
5
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612 **pept2funct** - https://unipept.ugent.be/apidocs/pept2funct
0
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613
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614 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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615
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616 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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617
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618 peptide: the peptide that matched this record
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619 total_protein_count: Total amount of proteins matched with the given peptide
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620 ec_number: EC-number associated with the current tryptic peptide.
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621 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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622 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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623 go_term: The GO-term associated with the current tryptic peptide.
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624 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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625 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
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626 code: InterPro entry code associated with the current tryptic peptide
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627 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
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628 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
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629 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
0
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630
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631
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632 **Attributions**
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633
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634 The Unipept metaproteomics analysis pipeline
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635 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
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636 Article first published online: 11 FEB 2015
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637 DOI: 10.1002/pmic.201400361
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638
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639 ]]></help>
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640 <citations>
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641 <citation type="doi">doi:10.1002/pmic.201400361</citation>
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642 </citations>
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643
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644 </tool>