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annotate unipept.xml @ 4:4953dcd7dd39 draft

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planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
author galaxyp
date Wed, 23 Jan 2019 09:16:38 -0500
parents 34758ab8aaa4
children 917fd3ebc223
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1 <tool id="unipept" name="Unipept" version="4.0.0">
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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>
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43 <requirement type="package" version="2.7">python</requirement>
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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 $output_go_tsv
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96 #end if
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97 #if 'unmatched' in str($selected_outputs).split(','):
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98 --unmatched $output_unmatched
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99 #end if
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100 ]]></command>
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101 <inputs>
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102 <conditional name="unipept">
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103 <param name="api" type="select" label="Unipept application" >
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104 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
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105 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
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106 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
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107 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
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108 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
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109 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
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110 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
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111 </param>
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112 <when value="pept2lca">
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113 <expand macro="equate_il" />
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114 <expand macro="extra">
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115 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
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116 </expand>
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117 <expand macro="names" />
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118 </when>
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119 <when value="pept2taxa">
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120 <expand macro="equate_il" />
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121 <expand macro="extra_true">
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122 <help>Return the complete lineage of each organism, and include ID fields.</help>
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123 </expand>
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124 <expand macro="names" />
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125 </when>
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126 <when value="pept2prot">
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127 <expand macro="equate_il" />
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128 <expand macro="extra">
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129 <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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130 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
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131 </help>
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132 </expand>
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133 </when>
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134 <when value="pept2ec">
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135 <expand macro="equate_il" />
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136 <expand macro="extra_true">
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137 <help>Return the name of the EC-number.
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138 </help>
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139 </expand>
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140 </when>
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141 <when value="pept2go">
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142 <expand macro="equate_il" />
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143 <expand macro="extra_true">
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144 <help>Return the name of the GO-term.
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145 </help>
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146 </expand>
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147 <expand macro="domains" />
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148 </when>
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149 <when value="pept2funct">
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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 EC-number and 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>
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157 <when value="peptinfo">
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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 EC-number and 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 <expand macro="names" />
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165 </when>
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166 </conditional>
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167 <conditional name="peptide_src">
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168 <param name="fmt" type="select" label="Peptides input format" >
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169 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
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170 <option value="tabular">tabular</option>
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171 <option value="fasta">fasta</option>
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172 <option value="mzid">mzid</option>
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173 <option value="pepxml">pepxml</option>
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174 </param>
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175 <when value="proteomic">
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176 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
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177 </when>
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178 <when value="tabular">
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179 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
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180 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
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181 </when>
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182 <when value="fasta">
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183 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
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184 </when>
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185 <when value="mzid">
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186 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
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187 </when>
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188 <when value="pepxml">
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189 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
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190 </when>
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191 </conditional>
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192 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
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193 <option value="tsv" selected="true">Tabular with one line per peptide</option>
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194 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
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195 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
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196 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
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197 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
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198 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
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199 <option value="unmatched">Unmatched peptides</option>
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200 </param>
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201 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
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202 </inputs>
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203 <outputs>
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204 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
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205 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
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206 <change_format>
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207 <when input="api" value="pept2prot" format="json" />
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208 </change_format>
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209 </data>
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210 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
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211 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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212 </data>
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213 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
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214 <filter>'tsv' in selected_outputs</filter>
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215 <actions>
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216 <action name="comment_lines" type="metadata" default="1" />
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217 <!--
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218 <conditional name="unipept.api">
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219 <when value="pept2funct">
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220 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
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221 </when>
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222 <when value="pept2go">
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223 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
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224 </when>
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225 <when value="pept2ec">
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226 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
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227 </when>
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228 </conditional>
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229 -->
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230 </actions>
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231 </data>
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232 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
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233 <filter>'csv' in selected_outputs</filter>
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234 </data>
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235 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
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236 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
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237 <actions>
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238 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
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239 </actions>
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240 </data>
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241 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
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242 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
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243 <actions>
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244 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
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245 </actions>
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246 </data>
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247 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
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248 <filter>'unmatched' in selected_outputs</filter>
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249 <actions>
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250 <action name="column_names" type="metadata" default="Unmatched Peptide" />
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251 </actions>
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252 </data>
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253 </outputs>
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254 <tests>
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255 <test>
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256 <param name="api" value="pept2lca"/>
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257 <param name="fmt" value="tabular"/>
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258 <param name="input_tsv" value="tryptic.tsv"/>
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259 <param name="column" value="2"/>
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260 <param name="extra" value="True"/>
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261 <param name="names" value="True"/>
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262 <param name="selected_outputs" value="tsv,unmatched"/>
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263 <output name="output_tsv">
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264 <assert_contents>
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265 <has_text text="Homininae" />
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266 </assert_contents>
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267 </output>
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268 <output name="output_unmatched">
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269 <assert_contents>
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270 <has_text text="QTAMAV" />
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271 </assert_contents>
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272 </output>
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273 </test>
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274 <test>
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275 <param name="api" value="pept2lca"/>
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276 <param name="fmt" value="fasta"/>
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277 <param name="input_fasta" value="peptide.fa"/>
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278 <param name="equate_il" value="True"/>
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279 <param name="extra" value="True"/>
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280 <param name="names" value="True"/>
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281 <param name="selected_outputs" value="json,tsv"/>
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282 <output name="output_json">
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283 <assert_contents>
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284 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
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285 </assert_contents>
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286 </output>
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287 <output name="output_tsv">
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288 <assert_contents>
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289 <has_text text="9606" />
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290 <has_text text="9596" />
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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="pept2taxa"/>
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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="False"/>
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300 <param name="names" value="False"/>
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301 <param name="selected_outputs" value="tsv"/>
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302 <output name="output_tsv">
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303 <assert_contents>
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304 <has_text text="sapiens" />
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305 <has_text text="paniscus" />
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306 <has_text text="Gorilla" />
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307 </assert_contents>
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308 </output>
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309 </test>
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310 <test>
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311 <param name="api" value="pept2funct"/>
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312 <param name="fmt" value="tabular"/>
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313 <param name="input_tsv" value="input.tsv"/>
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314 <param name="column" value="2"/>
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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="tsv,ec_tsv,go_tsv,unmatched"/>
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318 <output name="output_tsv">
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319 <assert_contents>
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320 <has_text text="GO:0004802" />
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321 <has_text text="2.2.1.1" />
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322 </assert_contents>
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323 </output>
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324 <output name="output_ec_tsv">
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325 <assert_contents>
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326 <has_text text="2.2.1.1" />
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327 </assert_contents>
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328 </output>
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329 <output name="output_go_tsv">
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330 <assert_contents>
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331 <has_text text="GO:0004802" />
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332 </assert_contents>
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333 </output>
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334 </test>
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335 </tests>
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336 <help><![CDATA[
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337 **Unipept**
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338
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339 Retrieve Uniprot and taxanomic information for trypic peptides.
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340
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341 Unipept API documentation - http://unipept.ugent.be/apidocs
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342
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343 **Input**
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344
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345 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
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346
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347 Processing deatils::
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348
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349 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
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350 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
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351 The match to the most specific tryptic fragment is reported.
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352
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353
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354 **Unipept APIs**
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355
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356 **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot
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357
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358 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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359
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360 By default, each object contains the following information fields extracted from the UniProt record::
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361
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362 peptide: the peptide that matched this record
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363 uniprot_id: the UniProt accession number of the matching record
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364 taxon_id: the NCBI taxon id of the organism associated with the matching record
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365
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366 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
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367
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368 taxon_name: the name of the organism associated with the matching UniProt record
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369 ec_references: a space separated list of associated EC numbers
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370 go_references: a space separated list of associated GO terms
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371 refseq_ids: a space separated list of associated RefSeq accession numbers
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372 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
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373 insdc_ids: a space separated list of associated insdc accession numbers
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374 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
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375
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376
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377 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa
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378
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379 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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380
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381 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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382
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383 peptide: the peptide that matched this record
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384 taxon_id: the NCBI taxon id of the organism associated with the matching record
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385 taxon_name: the name of the organism associated with the matching record
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386 taxon_rank: the taxonomic rank of the organism associated with the matching record
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387
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388 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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389
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390 superkingdom_id
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391 kingdom_id
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392 subkingdom_id
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393 superphylum_id
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394 phylum_id
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395 subphylum_id
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396 superclass_id
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397 class_id
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398 subclass_id
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399 infraclass_id
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400 superorder_id
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401 order_id
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402 suborder_id
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403 infraorder_id
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404 parvorder_id
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405 superfamily_id
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406 family_id
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407 subfamily_id
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408 tribe_id
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409 subtribe_id
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410 genus_id
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411 subgenus_id
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412 species_group_id
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413 species_subgroup_id
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414 species_id
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415 subspecies_id
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416 varietas_id
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417 forma_id
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418
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419
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420 **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca
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421
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422 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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423
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424 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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425
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426 peptide: the peptide that matched this record
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427 taxon_id: the NCBI taxon id of the organism associated with the matching record
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428 taxon_name: the name of the organism associated with the matching record
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429 taxon_rank: the taxonomic rank of the organism associated with the matching record
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430
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431 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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432
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433 superkingdom_id
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434 kingdom_id
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435 subkingdom_id
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436 superphylum_id
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437 phylum_id
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438 subphylum_id
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439 superclass_id
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440 class_id
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441 subclass_id
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442 infraclass_id
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443 superorder_id
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444 order_id
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445 suborder_id
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446 infraorder_id
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447 parvorder_id
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448 superfamily_id
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449 family_id
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450 subfamily_id
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451 tribe_id
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452 subtribe_id
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453 genus_id
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454 subgenus_id
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455 species_group_id
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457 species_id
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458 subspecies_id
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459 varietas_id
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460 forma_id
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461
4
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462 **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec
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463
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464 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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465
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466 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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467
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468 peptide: the peptide that matched this record
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469 total_protein_count: Total amount of proteins matched with the given peptide
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470 ec_number: EC-number associated with the current tryptic peptide.
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471 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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472 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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473
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474
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475 **pept2go** - http://unipept.ugent.be/apidocs/pept2go
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476
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477 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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478
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479 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
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480
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481 peptide: the peptide that matched this record
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482 total_protein_count: Total amount of proteins matched with the given peptide
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483 go_term: The GO-term associated with the current tryptic peptide.
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484 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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485 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
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486
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487
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488 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct
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489
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490 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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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 total_protein_count: Total amount of proteins matched with the given peptide
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496 ec_number: EC-number associated with the current tryptic peptide.
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497 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
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498 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
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499 go_term: The GO-term associated with the current tryptic peptide.
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500 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
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501 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
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502
0
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503
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504 **Attributions**
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505
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506 The Unipept metaproteomics analysis pipeline
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507 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
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508 Article first published online: 11 FEB 2015
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509 DOI: 10.1002/pmic.201400361
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510 http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04
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511
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512 ]]></help>
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513 <citations>
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514 <citation type="doi">doi:10.1002/pmic.201400361</citation>
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515 </citations>
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516
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517 </tool>