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comparison add_expression_data.xml @ 5:e919b55188ab draft

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planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
author proteore
date Wed, 02 Jan 2019 04:26:18 -0500
parents 3f9057cdfdde
children ea59f5750c51
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4:3f9057cdfdde 5:e919b55188ab
1 <tool id="rna_abbased_data" name="Add expression data" version="2018.12.12"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2019.01.02">
2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas] 2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 5 <requirement type="package" version="3.4.1">R</requirement>
6 </requirements> 6 </requirements>
22 22
23 ]]></command> 23 ]]></command>
24 24
25 <inputs> 25 <inputs>
26 <conditional name="inputtype"> 26 <conditional name="inputtype">
27 <param name="filetype" type="select" label="Enter your list of Ensembl gene ID"> 27 <param name="filetype" type="select" label="Enter your IDs (Ensembl gene ENSG IDs only)" help="Copy/paste or from a file (e.g. table)">
28 <option value="file_all" selected="true">Input file containing your IDs</option> 28 <option value="file_all" selected="true">Input file containing your IDs</option>
29 <option value="copy_paste">Copy/paste your list of IDs</option> 29 <option value="copy_paste">Copy/paste your list of IDs</option>
30 </param> 30 </param>
31 <when value="copy_paste"> 31 <when value="copy_paste">
32 <param name="genelist" type="text" label="Enter a list of identifiers"> 32 <param name="genelist" type="text" label="Enter a list of IDs">
33 <sanitizer> 33 <sanitizer>
34 <valid initial="string.printable"> 34 <valid initial="string.printable">
35 <remove value="&apos;"/> 35 <remove value="&apos;"/>
36 </valid> 36 </valid>
37 <mapping initial="none"> 37 <mapping initial="none">
39 </mapping> 39 </mapping>
40 </sanitizer> 40 </sanitizer>
41 </param> 41 </param>
42 </when> 42 </when>
43 <when value="file_all"> 43 <when value="file_all">
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."/> 44 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
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"/> 45 <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/>
46 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> 46 <param name="header" type="select" label="Does file contain header?" multiple="false" optional="false">
47 <option value="true" selected="true">Yes</option> 47 <option value="true" selected="true">Yes</option>
48 <option value="false" selected="false">No</option> 48 <option value="false" selected="false">No</option>
49 </param> 49 </param>
50 </when> 50 </when>
51 </conditional> 51 </conditional>
52 <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> 52 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
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"> 53 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" >
54 <option value="Gene" selected="true">Gene name</option> 54 <option value="Gene" selected="true">Gene name</option>
55 <option value="Gene description" selected="false">Gene description</option> 55 <option value="Gene description" selected="false">Gene description</option>
56 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> 56 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
57 <option value="Antibody">Antibody reference</option> 57 <option value="Antibody">Antibody reference</option>
58 <option value="RNA tissue category">RNA tissue category</option> 58 <option value="RNA tissue category">RNA tissue category</option>
59 <option value="Reliability (IH)">IH detection level</option> 59 <option value="Reliability (IH)">IH detection level</option>
60 <option value="Reliability (IF)">IF detection level</option> 60 <option value="Reliability (IF)">IF detection level</option>
61 <option value="Subcellular location">Subcellular location</option> 61 <option value="Subcellular location">Subcellular location</option>
62 <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> 62 <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option>
63 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> 63 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option>
64 </param> 64 </param>
75 <test> 75 <test>
76 <conditional name="inputtype"> 76 <conditional name="inputtype">
77 <param name="filetype " value="file_all"/> 77 <param name="filetype " value="file_all"/>
78 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> 78 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/>
79 <param name="column" value="c8"/> 79 <param name="column" value="c8"/>
80 <param name="header" value="TRUE"/> 80 <param name="header" value="true"/>
81 </conditional> 81 </conditional>
82 <section name="options"> 82 <section name="options">
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"/> 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"/>
84 </section> 84 </section>
85 <output name="output" file="Get_annotation_RNAseq.txt"/> 85 <output name="output" file="Get_annotation_RNAseq.txt"/>
86 </test> 86 </test>
87 </tests> 87 </tests>
88 88
89 <help><![CDATA[ 89 <help><![CDATA[
90 **Description**
90 91
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. 92 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.
93
94 -----
92 95
93 **Input** 96 **Input**
94 97
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. 98 Input can be either a list of Ensembl gene (ENSG) IDsds (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.
96 99
97 **Databases** 100 -----
98 101
99 HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz 102 **Parameters**
100 103
101 **Annotation** 104 "Select information to add to your list": choose by clicking the following information:
102 105
103 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) 106 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee)
104 107
105 - Gene description: entry description (full text) 108 - Gene description: entry description (full text)
106 109
118 121
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. 122 - 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.
120 123
121 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. 124 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
122 125
123 **Outputs** 126 -----
124 127
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. 128 **Output**
129
130 The output is a tabular file containing original columns and new columns including selected annotation.
131
132 -----
133
134 **Data sources (release date)**
135
136 HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz
126 137
127 ----- 138 -----
128 139
129 .. class:: infomark 140 .. class:: infomark
130 141
131 **Authors** 142 **Authors**
132 143
133 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 144 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
134 145
135 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 146 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
136 147
137 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 148 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
138 149
139 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 150 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
140 151