Mercurial > repos > bgruening > uniprot_rest_interface

annotate uniprot.xml @ 1:cd2a41c65447 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
author bgruening
date Fri, 14 Oct 2016 17:59:02 -0400
parents 48522382b6a4
children fe94765e8814
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1 <tool id="uniprot" name="UniProt" version="0.1">
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2 <description>ID mapping and retrieval</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.7">requests</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
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16 <command><![CDATA[
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17
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18 cut -f ${id_column} $infile > id_file.tabular &&
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19
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20 $__tool_directory__/uniprot.py
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21
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22 #if $tool.tool_choice == "retrieve":
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23 retrieve -f $tool.format $infile ./output
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24 #elif $tool.tool_choice == "map":
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25 map
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26
1
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27 #if $tool.from.category_FROM == "uniprot"
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28 '${tool.from.db_uniprot_FROM}'
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29 #elif $tool.from.category_FROM == "oseqdb"
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30 ${tool.from.db_oseqdb}
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31 #elif $tool.from.category_FROM == "3Dstrdb"
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32 ${tool.from.db_3Dstrdb}
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33 #elif $tool.from.category_FROM == "ppidb"
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34 ${tool.from.db_ppidb}
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35 #elif $tool.from.category_FROM == "chemistry"
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36 ${tool.from.db_chemistry}
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37 #elif $tool.from.category_FROM == "protfgdb"
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38 ${tool.from.db_protfgdb}
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39 #elif $tool.from.category_FROM == "polymorphismANDmutation"
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40 ${tool.from.db_polymorphismANDmutation}
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41 #elif $tool.from.category_FROM == "2DgelDB"
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42 ${tool.from.db_2DgelDB}
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43 #elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
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44 ${tool.from.db_ProtocolsMaterialsDB}
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45 #elif $tool.from.category_FROM == "GenomeAnnotationDB"
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46 ${tool.from.db_GenomeAnnotationDB}
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47 #elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
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48 ${tool.from.db_OrganismSpecificGeneDB}
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49 #elif $tool.from.category_FROM == "phylogenomic"
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50 ${tool.from.db_phylogenomic}
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51 #elif $tool.from.category_FROM == "EnzymePathwayDB"
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52 ${tool.from.db_EnzymePathwayDB}
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53 #elif $tool.from.category_FROM == "GeneExpression"
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54 ${tool.from.db_GeneExpression}
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55 #elif $tool.from.category_FROM == "other"
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56 ${tool.from.db_other}
0
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57 #end if
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58
1
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59 #if $tool.to.category_TO == "uniprot"
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60 ${tool.to.db_uniprot_TO}
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61 #elif $tool.to.category_TO == "oseqdb"
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62 ${tool.to.db_oseqdb}
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63 #elif $tool.to.category_TO == "3Dstrdb"
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64 ${tool.to.db_3Dstrdb}
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65 #elif $tool.to.category_TO == "ppidb"
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66 ${tool.to.db_ppidb}
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67 #elif $tool.to.category_TO == "chemistry"
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68 ${tool.to.db_chemistry}
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69 #elif $tool.to.category_TO == "protfgdb"
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70 ${tool.to.db_protfgdb}
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71 #elif $tool.to.category_TO == "polymorphismANDmutation"
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72 ${tool.to.db_polymorphismANDmutation}
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73 #elif $tool.to.category_TO == "2DgelDB"
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74 ${tool.to.db_2DgelDB}
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75 #elif $tool.to.category_TO == "ProtocolsMaterialsDB"
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76 ${tool.to.db_ProtocolsMaterialsDB}
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77 #elif $tool.to.category_TO == "GenomeAnnotationDB"
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78 ${tool.to.db_GenomeAnnotationDB}
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79 #elif $tool.to.category_TO == "OrganismSpecificGeneDB"
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80 ${tool.to.db_OrganismSpecificGeneDB}
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81 #elif $tool.to.category_TO == "phylogenomic"
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82 ${tool.to.db_phylogenomic}
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83 #elif $tool.to.category_TO == "EnzymePathwayDB"
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84 ${tool.to.db_EnzymePathwayDB}
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85 #elif $tool.to.category_TO == "GeneExpression"
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86 ${tool.to.db_GeneExpression}
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87 #elif $tool.to.category_TO == "other"
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88 ${tool.to.db_other}
0
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89 #end if
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90
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91 id_file.tabular
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92 ./output
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93 #end if
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94
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95 ]]></command>
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96 <inputs>
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97 <param name="infile" type="data" format="tabular" label="Input file with IDs"
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98 help="One ID in each line."/>
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99 <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/>
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100
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101 <conditional name="tool">
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102 <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help="">
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103 <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option>
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104 <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option>
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105 </param>
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106 <when value="map">
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107 <conditional name="from">
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108 <expand macro="macro-category_FROM"/>
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109 <when value="uniprot">
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110 <expand macro="macro-db_uniprot_FROM"/>
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111 </when>
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112 <when value="oseqdb">
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113 <expand macro="macro-db_oseqdb"/>
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114 </when>
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115 <when value="3Dstrdb">
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116 <expand macro="macro-db_3Dstrdb"/>
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117 </when>
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118 <when value="ppidb">
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119 <expand macro="macro-db_ppidb"/>
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120 </when>
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121 <when value="chemistry">
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122 <expand macro="macro-db_chemistry"/>
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123 </when>
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124 <when value="protfgdb">
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125 <expand macro="macro-db_protfgdb"/>
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126 </when>
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127 <when value="polymorphismANDmutation">
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128 <expand macro="macro-db_polymorphismANDmutation"/>
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129 </when>
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130 <when value="2DgelDB">
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131 <expand macro="macro-db_2DgelDB"/>
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132 </when>
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133 <when value="ProtocolsMaterialsDB">
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134 <expand macro="macro-db_ProtocolsMaterialsDB"/>
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135 </when>
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136 <when value="GenomeAnnotationDB">
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137 <expand macro="macro-db_GenomeAnnotationDB"/>
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138 </when>
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139 <when value="OrganismSpecificGeneDB">
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140 <expand macro="macro-db_OrganismSpecificGeneDB"/>
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141 </when>
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142 <when value="phylogenomic">
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143 <expand macro="macro-db_phylogenomic"/>
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144 </when>
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145 <when value="EnzymePathwayDB">
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146 <expand macro="macro-db_EnzymePathwayDB"/>
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147 </when>
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148 <when value="GeneExpression">
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149 <expand macro="macro-db_GeneExpression"/>
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150 </when>
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151 <when value="other">
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152 <expand macro="macro-db_other"/>
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153 </when>
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154 </conditional>
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155 <conditional name="to">
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156 <expand macro="macro-category_TO"/>
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157 <when value="uniprot">
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158 <expand macro="macro-db_uniprot_TO"/>
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159 </when>
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160 <when value="oseqdb">
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161 <expand macro="macro-db_oseqdb"/>
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162 </when>
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163 <when value="3Dstrdb">
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164 <expand macro="macro-db_3Dstrdb"/>
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165 </when>
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166 <when value="ppidb">
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167 <expand macro="macro-db_ppidb"/>
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168 </when>
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169 <when value="chemistry">
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170 <expand macro="macro-db_chemistry"/>
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171 </when>
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172 <when value="protfgdb">
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173 <expand macro="macro-db_protfgdb"/>
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174 </when>
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175 <when value="polymorphismANDmutation">
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176 <expand macro="macro-db_polymorphismANDmutation"/>
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177 </when>
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178 <when value="2DgelDB">
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179 <expand macro="macro-db_2DgelDB"/>
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180 </when>
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181 <when value="ProtocolsMaterialsDB">
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182 <expand macro="macro-db_ProtocolsMaterialsDB"/>
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183 </when>
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184 <when value="GenomeAnnotationDB">
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185 <expand macro="macro-db_GenomeAnnotationDB"/>
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186 </when>
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187 <when value="OrganismSpecificGeneDB">
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188 <expand macro="macro-db_OrganismSpecificGeneDB"/>
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189 </when>
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190 <when value="phylogenomic">
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191 <expand macro="macro-db_phylogenomic"/>
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192 </when>
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193 <when value="EnzymePathwayDB">
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194 <expand macro="macro-db_EnzymePathwayDB"/>
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195 </when>
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196 <when value="GeneExpression">
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197 <expand macro="macro-db_GeneExpression"/>
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198 </when>
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199 <when value="other">
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200 <expand macro="macro-db_other"/>
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201 </when>
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202 </conditional>
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203 </when>
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204 <when value="retrieve">
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205 <param name="format" type="select" label="Choose format of output file" help="">
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206 <option value="fasta">fasta</option>
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207 <option value="gff">gff</option>
1
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208 <option value="txt">Text</option>
0
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209 </param>
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210 </when>
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211 </conditional>
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212 </inputs>
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213 <outputs>
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214 <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
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215 label="${tool.name} on ${on_string} (retrieve output)">
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216 <filter>tool['tool_choice'] == 'retrieve'</filter>
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217 <filter>tool['format'] == 'fasta'</filter>
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218 </data>
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219 <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
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220 label="${tool.name} on ${on_string} (retrieve output)">
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221 <filter>tool['tool_choice'] == 'retrieve'</filter>
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222 <filter>tool['format'] == 'gff'</filter>
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223 </data>
1
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224 <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
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225 label="${tool.name} on ${on_string} (retrieve output)">
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226 <filter>tool['tool_choice'] == 'retrieve'</filter>
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227 <filter>tool['format'] == 'txt'</filter>
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228 </data>
0
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229 <data name="outfile_map" format="tabular" from_work_dir="./output"
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230 label="${tool.name} on ${on_string} (map output)">
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231 <filter>tool['tool_choice'] == 'map'</filter>
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232 </data>
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233 </outputs>
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234 <tests>
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235 <test>
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236 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
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237 <param name="id_column" value="c1"/>
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238 <param name="format" value="fasta"/>
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239 <param name="tool_choice" value="retrieve"/>
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240 <output name="outfile_retrieve" file="test1_retrieve.fasta" ftype="fasta"/>
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241 </test>
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242 <test>
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243 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
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244 <param name="id_column" value="c1"/>
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245 <param name="format" value="gff"/>
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246 <param name="tool_choice" value="retrieve"/>
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247 <output name="outfile_retrieve" file="test2_retrieve.gff" ftype="gff"/>
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248 </test>
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249 <test>
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250 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
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251 <param name="id_column" value="c1"/>
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252 <param name="tool_choice" value="map"/>
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253 <param name="category_FROM" value="uniprot"/>
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254 <param name="db_uniprot_FROM" value="ID"/>
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255 <param name="category_TO" value="uniprot"/>
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256 <param name="db_uniprot_TO" value="GENENAME"/>
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257 <output name="outfile_map" file="test1_map.tab" ftype="tabular"/>
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258 </test>
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259 <test>
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260 <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
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261 <param name="id_column" value="c1"/>
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262 <param name="tool_choice" value="map"/>
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263 <param name="category_FROM" value="oseqdb"/>
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264 <param name="db_oseqdb" value="REFSEQ_NT_ID"/>
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265 <param name="category_TO" value="uniprot"/>
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266 <param name="db_uniprot_TO" value="ID"/>
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267 <output name="outfile_map" file="test2_map.tab" ftype="tabular"/>
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268 </test>
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269 </tests>
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270 <help><![CDATA[
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271
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272 .. class:: infomark
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273
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274 **What it does**
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275
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276 This tool provides access to the UniProt API. You can retrieve sequence informations given a list of sequence identifiers or map
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277 identifiers between different databases.
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278 Hence, this tool offers you two modes: *map* and *retrieve*.
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279
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280 -----
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281
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282 **INPUT**
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283
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284 The input is a list of IDs.
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285
1
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286 *Example*::
0
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287
1
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288 Q0P8A9
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289 A0A077ZHN8
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290 A0A077ZFY8
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291 M5B8V9
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292 M5BAG7
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293 S0DS17
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294 ....
0
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295
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296 -----
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297
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298 **MAP OUTPUT EXAMPLES**
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299
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300 FROM refseq TO embl::
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301
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302 From To
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303 NM_130786 A1BG_HUMAN
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304 NM_130786 V9HWD8_HUMAN
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305 NM_001087 A0A024R410_HUMAN
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306 NM_001087 AAMP_HUMAN
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307
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308 FROM uniprot TO genename::
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309
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310 From To
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311 Q0P8A9 fdhC
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312 A0A077ZHN8 TTRE_0000819801
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313 A0A077ZFY8 TTRE_0000758701
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314 M5B8V9 CMN_01519
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315 M5BAG7 cydC
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316 S0DS17 FFUJ_00006
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317 A0A077Z587 TTRE_0000309301
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318 Q13685 AAMP
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319 O14639 ABLIM1
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320
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321 -----
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322
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323 **RETRIEVE OUTPUT EXAMPLES**
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324
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325 retrieve gff::
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326
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327 #gff-version 3
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328 #sequence-region S0DS17 1 369
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329 #sequence-region M5BAG7 1 563
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330 #sequence-region A0A077Z587 1 772
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331 #sequence-region A0A077ZFY8 1 973
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332 #sequence-region O14639 1 778
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333 O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1
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334 O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125
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335 O14639 UniProtKB Domain 156 216 . . . Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125
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336 O14639 Un...
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337
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338 retrieve fasta::
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339
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340 >tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1
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341 MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS
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342 YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKY...
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343 >tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1
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344 MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG
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345 VRAFALGRAAFRYLERITSHDAAFRALATLRV...
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346 >tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1
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347 MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD
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348 VIKDVNGSRIDSRELCRDLIRTHKVLTV...
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349
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350 -----
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351
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352 This tool is based on the work `Jan Rudolph`_ and the UniProt API.
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353
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354 .. _Jan Rudolph: https://github.com/jdrudolph/uniprot
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355
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356 ]]></help>
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357 <citations>
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358 <citation type="doi">10.1093/nar/gku989</citation>
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359 </citations>
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360 </tool>