Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_data.xml @ 12:dbeabf9bf091 draft

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planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty
author proteore
date Thu, 07 Mar 2019 09:08:33 -0500
parents e109cacd75b2
children 0b279190f90d
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11:e109cacd75b2 12:dbeabf9bf091
1 <tool id="rna_abbased_data" name="Add expression data" version="2019.01.02"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2019.03.07">
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 IDs (Ensembl gene ENSG IDs only)" help="Copy/paste or from a file (e.g. table)"> 27 <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)">
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 IDs"> 32 <param name="genelist" type="text" label="Enter a list of IDs">
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="Select your file" help=""/> 44 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
45 <param name="column" type="text" label="Column 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 file contain header?" multiple="false" optional="false"> 46 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
47 <option value="true" selected="true">Yes</option>
48 <option value="false" selected="false">No</option>
49 </param> 47 </param>
48 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?"/>
50 </when> 49 </when>
51 </conditional> 50 </conditional>
52 <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> 51 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
53 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > 52 <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> 53 <option value="Gene" selected="true">Gene name</option>
93 92
94 ----- 93 -----
95 94
96 **Input** 95 **Input**
97 96
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. 97 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.
99 98
100 ----- 99 -----
101 100
102 **Parameters** 101 **Parameters**
103 102
125 124
126 ----- 125 -----
127 126
128 **Output** 127 **Output**
129 128
130 The output is a tabular file containing original columns and new columns including selected annotation. 129 The output is a tabular file containing initial columns and new columns with annotation from HPA.
131 130
132 ----- 131 -----
133 132
134 **Data sources (release date)** 133 **Data sources (release date)**
135 134
136 HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz 135 HPA source file (Human Protein Atlas version 18.1): http://www.proteinatlas.org/download/proteinatlas.tab.gz
137 136
138 ----- 137 -----
139 138
140 .. class:: infomark 139 .. class:: infomark
141 140
142 **Authors** 141 **Authors**
143 142
144 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 143 Lisa Peru, David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
145 144
146 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 145 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
147 146
148 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 147 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
149 148