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comparison add_expression_data.xml @ 6:ea59f5750c51 draft

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 03:56:26 -0400
parents e919b55188ab
children fda784211e3a
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5:e919b55188ab 6:ea59f5750c51
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="2019.06.27">
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.
98
99 .. class:: warningmark
100
101 In copy/paste mode, the number of IDs considered in input is limited to 5000.
99 102
100 ----- 103 -----
101 104
102 **Parameters** 105 **Parameters**
103 106
125 128
126 ----- 129 -----
127 130
128 **Output** 131 **Output**
129 132
130 The output is a tabular file containing original columns and new columns including selected annotation. 133 The output is a tabular file containing initial columns and new columns with annotation from HPA.
131 134
132 ----- 135 -----
133 136
134 **Data sources (release date)** 137 **Data sources (release date)**
135 138
136 HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz 139 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
137 140
138 ----- 141 -----
139 142
140 .. class:: infomark 143 .. class:: infomark
141 144
142 **Authors** 145 **Authors**
143 146
144 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 147 Lisa Perus, David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
145 148
146 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 149 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
147 150
148 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 151 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
149 152
150 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 153 Help: contact@proteore.org for any questions or concerns about this tool.
151 154
152 ]]></help> 155 ]]></help>
153 156
154 <citations> 157 <citations>
155 </citations> 158 </citations>