Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_data.xml @ 4:3f9057cdfdde draft

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planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
author proteore
date Thu, 13 Dec 2018 03:56:46 -0500
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children e919b55188ab
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1 <tool id="rna_abbased_data" name="Add expression data" version="2018.12.12">
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2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
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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 #if $inputtype.filetype == "copy_paste":
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14 Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output'
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16 #else
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17
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18 Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output'
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19
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20 #end if
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23 ]]></command>
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24
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25 <inputs>
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26 <conditional name="inputtype">
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27 <param name="filetype" type="select" label="Enter your list of Ensembl gene ID">
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28 <option value="file_all" selected="true">Input file containing your IDs</option>
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29 <option value="copy_paste">Copy/paste your list of IDs</option>
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30 </param>
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31 <when value="copy_paste">
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32 <param name="genelist" type="text" label="Enter a list of identifiers">
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33 <sanitizer>
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34 <valid initial="string.printable">
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35 <remove value="&apos;"/>
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36 </valid>
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37 <mapping initial="none">
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38 <add source="&apos;" target="__sq__"/>
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39 </mapping>
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40 </sanitizer>
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41 </param>
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42 </when>
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43 <when value="file_all">
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44 <param name="genelist" type="data" format="txt,tabular" label="Choose your file" help="This file must imperatively have 1 column filled with Ensembl Gene IDs (ENSG). Please use the ID_Converter tool if this is not the case."/>
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45 <param name="column" type="text" label="Please specify the column where are your Ensembl gene IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/>
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46 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false">
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47 <option value="true" selected="true">Yes</option>
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48 <option value="false" selected="false">No</option>
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49 </param>
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50 </when>
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51 </conditional>
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52 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
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53 <param name="hpaparams" type="select" label="Choose the information from RNAseq/ab-based data you want to add to your list (see below for details)" multiple="True" display="checkboxes">
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54 <option value="Gene" selected="true">Gene name</option>
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55 <option value="Gene description" selected="false">Gene description</option>
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56 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
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57 <option value="Antibody">Antibody reference</option>
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58 <option value="RNA tissue category">RNA tissue category</option>
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59 <option value="Reliability (IH)">IH detection level</option>
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60 <option value="Reliability (IF)">IF detection level</option>
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61 <option value="Subcellular location">Subcellular location</option>
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62 <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option>
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63 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option>
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64 </param>
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65 </section>
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66
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67 </inputs>
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69
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70 <outputs>
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71 <data name="output" format="tsv" label=""/>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <conditional name="inputtype">
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77 <param name="filetype " value="file_all"/>
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78 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/>
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79 <param name="column" value="c8"/>
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80 <param name="header" value="TRUE"/>
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81 </conditional>
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82 <section name="options">
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83 <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/>
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84 </section>
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85 <output name="output" file="Get_annotation_RNAseq.txt"/>
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86 </test>
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87 </tests>
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88
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89 <help><![CDATA[
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90
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91 This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list.
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92
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93 **Input**
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94
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95 Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.
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96
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97 **Databases**
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98
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99 HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz
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100
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101 **Annotation**
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102
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103 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee)
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104
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105 - Gene description: entry description (full text)
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106
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107 - Evidence: at protein level, at transcript level or no evidence
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108
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109 - Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF
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110
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111 - RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .
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112
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113 - IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
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114
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115 - IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih .
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116
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117 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
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118
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119 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.
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120
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121 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
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122
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123 **Outputs**
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124
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125 The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose.
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126
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127 -----
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128
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129 .. class:: infomark
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130
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131 **Authors**
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132
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133 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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134
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135 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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136
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137 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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138
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139 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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140
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141 ]]></help>
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142
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143 <citations>
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144 </citations>
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145
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146 </tool>