Mercurial > repos > proteore > proteore_prot_features
annotate add_protein_features.xml @ 9:0b46a7aead62 draft
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author | proteore |
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date | Tue, 18 Dec 2018 08:26:55 -0500 |
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children | 4de4f6359820 |
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1 <tool id="prot_features" name="Add protein features" version="2018.12.18"> |
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2 <description>[neXtProt] |
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3 </description> |
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4 <requirements> |
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5 <requirement type="package" version="3.4.1">R</requirement> |
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6 </requirements> |
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7 <stdio> |
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8 <exit_code range="1:" /> |
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9 </stdio> |
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10 <command><![CDATA[ |
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11 |
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12 Rscript $__tool_directory__/add_protein_features.R |
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13 --inputtype="$inputtype.filetype" |
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14 --input='$inputtype.genelist' |
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15 |
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16 #if $inputtype.filetype == "file" |
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17 --column='$inputtype.column' |
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18 --header=$inputtype.header |
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19 #end if |
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20 |
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21 --type='$idtype' |
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22 --pc_features='$Nextprot_params.pc_features' |
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23 --localization='$Nextprot_params.localization' |
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24 --diseases_info='$Nextprot_params.diseases_info' |
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25 --output='$output' |
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26 --nextprot=$__tool_directory__/tool-data/result_nextprot.txt |
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27 |
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28 ]]></command> |
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29 |
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30 <inputs> |
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31 <conditional name="inputtype"> |
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32 <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" > |
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33 <option value="file" selected="true">Input file containing your IDs </option> |
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34 <option value="copy_paste">Copy/paste your list of IDs</option> |
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35 </param> |
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36 <when value="copy_paste"> |
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37 <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0"> |
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38 <sanitizer invalid_char=""> |
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39 <valid initial="string.printable"> |
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40 <remove value="'"/> |
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41 </valid> |
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42 <mapping initial="none"> |
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43 <add source="'" target="__sq__"/> |
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44 <add source=" " target=""/> |
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45 <add source="
" target=""/> |
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46 <add source="
" target=""/> |
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47 <add source="	" target=""/> |
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48 </mapping> |
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49 </sanitizer> |
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50 </param> |
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51 </when> |
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52 <when value="file"> |
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53 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> |
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54 <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> |
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55 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> |
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56 |
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57 </when> |
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58 </conditional> |
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59 |
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60 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> |
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61 <option value="Uniprot_AC" selected="true">Uniprot accession number</option> |
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62 <option value="NextprotID" selected="false">neXtProt IDs</option> |
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63 </param> |
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64 <section name="Nextprot_params" title="Select features" expanded="True"> |
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65 <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="true"> |
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66 <option value="SeqLength" selected="false">Sequence Length</option> |
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67 <option value="MW" selected="false">Molecular Weight</option> |
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68 <option value="IsoPoint" selected="false">Isoelectric point</option> |
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69 <option value="TMDomains" selected="false">Number of transmembrane domains</option> |
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70 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> |
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71 </param> |
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72 |
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73 <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> |
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74 <option value="Chr" selected="false">Chromosome</option> |
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75 <option value="SubcellLocations" selected="false">Subcellular Location</option> |
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76 </param> |
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77 |
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78 <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" /> |
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79 |
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80 </section> |
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81 |
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82 </inputs> |
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83 |
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84 |
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85 <outputs> |
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86 <data name="output" format="tsv" label="Add_information_from_neXtProt on ${inputtype.genelist.name}"> |
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87 <filter>inputtype=="file"</filter> |
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88 </data> |
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89 <data name="output" format="tsv" label="Add_information_from_neXtProt"/> |
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90 </outputs> |
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91 |
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92 <tests> |
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93 <test> |
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94 <conditional name="inputtype"> |
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95 <param name="filetype " value="file"/> |
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96 <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv"/> |
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97 <param name="column" value="c1"/> |
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98 <param name="header" value="true"/> |
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99 </conditional> |
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100 |
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101 <param name="idtype" value="uniprot"/> |
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102 |
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103 <section name="Nextprot_params"> |
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104 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> |
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105 <param name="localization" value="Chr,SubcellLocations"/> |
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106 <param name="diseases_info" value="true"/> |
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107 </section> |
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108 |
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109 <output name="output" file="Add_information_from_neXtProt.tsv"/> |
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110 </test> |
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111 </tests> |
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112 |
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113 <help><![CDATA[ |
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114 |
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115 **Description** |
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116 |
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117 This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list. |
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118 |
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119 ----- |
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120 |
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121 **Input** |
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122 |
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123 A list of of Uniprot (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool. |
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124 |
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125 ----- |
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126 |
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127 **Parameters** |
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128 |
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129 "Select fetures": three categories of annotation can be retrieved; physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. |
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130 |
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131 ----- |
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132 |
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133 **Output** |
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134 |
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135 Output is a tabular file containing both original columns and new columns including the annotation requested. |
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136 |
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137 ----- |
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138 |
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139 **Data source (release date)** |
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140 |
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141 Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release January 2018) |
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142 |
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143 using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) |
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144 |
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145 ----- |
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146 |
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147 .. class:: infomark |
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148 |
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149 **Authors** |
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150 |
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151 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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152 |
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153 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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154 |
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155 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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156 |
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157 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
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158 |
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159 ]]></help> |
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160 <citations> |
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161 </citations> |
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162 |
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163 </tool> |