Mercurial > repos > proteore > proteore_prot_features

annotate prot_features.xml @ 1:2fc914ab92f5 draft

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author proteore
date Tue, 04 Dec 2018 05:48:58 -0500
parents b455ec3f4f33
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1
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1 <tool id="prot_features" name="Add human protein features" version="2018.12.04">
0
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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 $__tool_directory__/protein_features.R
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13 --inputtype="$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="Select your type of input file">
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33 <option value="file" selected="true">Input file containing your identifiers (neXtProt or Uniprot ID)</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 identifiers 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="&apos;"/>
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41 </valid>
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42 <mapping initial="none">
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43 <add source="&apos;" target="__sq__"/>
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44 <add source="&#x20;" target=""/>
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45 <add source="&#xA;" target=""/>
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46 <add source="&#xD;" target=""/>
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47 <add source="&#x9;" 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="Choose a file that contains your list of IDs" help="This file must imperatively have 1 column filled with IDs consistent with the neXtprot database (Uniprot accession number or neXtProt ID). If this is not the case, please use the ID_Converter tool."/>
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54 <param name="column" type="text" label="Please specify the column where are your 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 your input file have a 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 your input 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 of interest (compulsory step)" expanded="True">
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65 <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="Choose the information you want to add to your data from Nextprot" 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="Choose the information you want to add to your data from Nextprot" 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="Diseases informations" />
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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 This tool add annotation (protein features) from neXtProt database (knowledge base on human proteins) to your protein IDs list.
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116
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117 **Input**
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118
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119 Input can be a file containing multiple fields but 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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120
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121 **Databases**
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122
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123 Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release Human 2018-1)
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124
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125 using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017)
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126
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127 **Outputs**
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128
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129 The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.
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130
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131 -----
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132
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133 .. class:: infomark
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134
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135 **Authors**
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136
1
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137 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0
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138
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139 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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140
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141 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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142
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143 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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144
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145 ]]></help>
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146 <citations>
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147 </citations>
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148
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149 </tool>