Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_data.xml @ 15:64681d9836e7 draft

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"planemo upload commit f04dc917acc0f3f14c950b139eb09a045e42fd00-dirty"
author proteore
date Thu, 23 Jan 2020 11:14:08 +0000
parents 778f7281ccba
children 0ce8b8d2322f
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1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.23.3">
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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="3.4.4">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 $__tool_directory__/add_expression_HPA.R
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13 --input='$inputtype.genelist'
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14 --select='$options.hpaparams'
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15 --output='$output'
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16
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17 #if $inputtype.filetype == "copy_paste":
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18 --inputtype="copypaste"
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19 #else
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20 --inputtype="tabfile"
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21 --header='$inputtype.header'
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22 --column='$inputtype.column'
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23 #end if
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24
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25 #if "protein_atlas" in str($ref_file).split("/")
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26 --atlas="$ref_file"
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27 #else
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28 --atlasf="$__tool_directory__/$ref_file"
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29 #end if
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30
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31 ]]></command>
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32
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33 <inputs>
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34 <param name="ref_file" type="select" label="HPA source file version" >
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35 <options from_data_table="proteore_protein_full_atlas">
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36 <filter type="sort_by" column="0"/>
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37 </options>
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38 </param>
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39 <conditional name="inputtype">
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40 <param name="filetype" type="select" label="Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)">
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41 <option value="file_all" selected="true">Input file containing your IDs</option>
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42 <option value="copy_paste">Copy/paste your list of IDs</option>
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43 </param>
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44 <when value="copy_paste">
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45 <param name="genelist" type="text" label="Enter a list of IDs">
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46 <sanitizer>
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47 <valid initial="string.printable">
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48 <remove value="&apos;"/>
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49 </valid>
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50 <mapping initial="none">
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51 <add source="&apos;" target="__sq__"/>
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52 </mapping>
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53 </sanitizer>
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54 </param>
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55 </when>
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56 <when value="file_all">
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57 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
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58 <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1">
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59 <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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60 </param>
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61 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?"/>
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62 </when>
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63 </conditional>
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64 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
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65 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" >
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66 <option value="Gene" selected="true">Gene name</option>
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67 <option value="Gene description" selected="false">Gene description</option>
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68 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
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69 <option value="Antibody">Antibody reference</option>
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70 <option value="RNA tissue specificity">RNA tissue category</option>
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71 <option value="Reliability (IH)">IH detection level</option>
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72 <option value="Reliability (IF)">IF detection level</option>
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73 <option value="Subcellular location">Subcellular location</option>
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74 <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option>
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75 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option>
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76 </param>
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77 </section>
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78
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79 </inputs>
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80
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81
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82 <outputs>
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83 <data name="output" format="tsv" label=""/>
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <conditional name="inputtype">
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89 <param name="filetype " value="file_all"/>
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90 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/>
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91 <param name="column" value="c8"/>
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92 <param name="header" value="true"/>
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93 </conditional>
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94 <section name="options">
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95 <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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96 </section>
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97 <output name="output" file="Get_annotation_RNAseq.txt"/>
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98 </test>
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99 </tests>
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100
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101 <help><![CDATA[
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102 **Description**
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103
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104 This tool adds expression annotation (RNAseq- or antibody-based experimental data - see "Parameters" below) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your gene/protein list.
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105
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106 -----
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107
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108 **Input**
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109
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110 Input can be either a list of Ensembl gene (ENSG) IDs (copy/paste mode) or a file containing multiple fields 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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111
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112 .. class:: warningmark
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113
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114 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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115
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116 -----
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117
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118 **Parameters**
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119
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120 "Select information to add to your list": choose by clicking the following information:
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121
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122 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee)
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123
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124 - Gene description: entry description (full text)
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125
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126 - Evidence: at protein level, at transcript level or no evidence
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127
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128 - Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF
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129
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130 - 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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131
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132 - 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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133
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134 - 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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135
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136 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
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137
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138 - 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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139
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140 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
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141
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142 -----
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143
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144 **Output**
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145
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146 The output is a tabular file containing initial columns and new columns with annotation from HPA.
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147
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148 -----
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149
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150 **Data sources (release date)**
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151
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152 HPA source file (data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38): http://www.proteinatlas.org/download/proteinatlas.tab.gz
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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 Lisa Perus, David Christiany, 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 Help: contact@proteore.org for any questions or concerns about this tool.
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167
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168 ]]></help>
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169
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170 <citations>
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171 </citations>
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172
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173 </tool>