Mercurial > repos > proteore > proteore_prot_features

annotate add_protein_features.xml @ 6:a37b623bcd7c draft

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author proteore
date Mon, 11 Mar 2019 04:40:52 -0400
parents bb4a5f1b415f
children 69c70e45d5ab
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1 <tool id="prot_features" name="Add protein features" version="2019.03.10">
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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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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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16 #if $inputtype.filetype == "file"
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17 --column='$inputtype.column'
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18 --header=$inputtype.header
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19 #end if
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21 --type='$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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27 #if 'nextprot_ref' in str($ref_file).split("/")
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28 --nextprot="$ref_file"
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29 #else
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30 --nextprot="$__tool_directory__/$ref_file"
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31 #end if
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33 ]]></command>
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34
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35 <inputs>
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36 <conditional name="inputtype">
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37 <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" >
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38 <option value="file" selected="true">Input file containing your IDs </option>
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39 <option value="copy_paste">Copy/paste your list of IDs</option>
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40 </param>
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41 <when value="copy_paste">
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42 <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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43 <sanitizer invalid_char="">
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44 <valid initial="string.printable">
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45 <remove value="&apos;"/>
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46 </valid>
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47 <mapping initial="none">
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48 <add source="&apos;" target="__sq__"/>
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49 <add source="&#x20;" target=""/>
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50 <add source="&#xA;" target=""/>
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51 <add source="&#xD;" target=""/>
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52 <add source="&#x9;" target=""/>
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53 </mapping>
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54 </sanitizer>
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55 </param>
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56 </when>
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57 <when value="file">
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58 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
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59 <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
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60 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
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61 </param>
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62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
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63 </when>
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64 </conditional>
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65
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66 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false">
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67 <option value="Uniprot_AC" selected="true">Uniprot accession number</option>
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68 <option value="NextprotID" selected="false">neXtProt IDs</option>
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69 </param>
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70 <section name="Nextprot_params" title="Select features" expanded="True">
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71 <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false">
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72 <option value="SeqLength" selected="false">Sequence Length</option>
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73 <option value="MW" selected="false">Molecular Weight</option>
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74 <option value="IsoPoint" selected="false">Isoelectric point</option>
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75 <option value="TMDomains" selected="false">Number of transmembrane domains</option>
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76 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
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77 </param>
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78
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79 <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true">
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80 <option value="Chr" selected="false">Chromosome</option>
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81 <option value="SubcellLocations" selected="false">Subcellular Location</option>
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82 </param>
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83
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84 <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
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85
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86 </section>
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87 <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
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88 <options from_data_table="proteore_nextprot_ref"/>
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89 </param>
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90
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91 </inputs>
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94 <outputs>
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95 <data name="output" format="tsv" label="Add_information_from_neXtProt on ${inputtype.genelist.name}">
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96 <filter>inputtype=="file"</filter>
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97 </data>
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98 <data name="output" format="tsv" label="Add_information_from_neXtProt"/>
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99 </outputs>
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100
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101 <tests>
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102 <test>
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103 <conditional name="inputtype">
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104 <param name="filetype " value="file"/>
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105 <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv"/>
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106 <param name="column" value="c1"/>
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107 <param name="header" value="true"/>
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108 </conditional>
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109
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110 <param name="idtype" value="uniprot"/>
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111
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112 <section name="Nextprot_params">
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113 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/>
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114 <param name="localization" value="Chr,SubcellLocations"/>
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115 <param name="diseases_info" value="true"/>
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116 </section>
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117
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118 <output name="output" file="Add_information_from_neXtProt.tsv"/>
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119 </test>
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120 </tests>
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121
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122 <help><![CDATA[
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123
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124 **Description**
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125
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126 This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
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127
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128 -----
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129
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130 **Input**
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131
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132 A list of of Uniprot Accession Number (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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133
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134 -----
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135
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136 **Parameters**
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137
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138 "Select features": 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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139
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140 -----
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141
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142 **Output**
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143
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144 Output is a tabular file containing both original columns and new columns including the annotation requested.
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145
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146 -----
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147
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148 **Data source (release date)**
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149
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150 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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151
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152 using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017)
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153
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154 -----
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155
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156 .. class:: infomark
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157
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158 **Authors**
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159
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160 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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161
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162 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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163
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164 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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165
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166 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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167
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168 ]]></help>
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169 <citations>
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170 </citations>
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171
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172 </tool>