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author proteore
date Thu, 13 Dec 2018 03:59:41 -0500
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1 <tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2018.12.12">
2 <description>[Human Protein Atlas](no input required)</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">R</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command interpreter="Rscript">
10 $__tool_directory__/Build_tissue-specific_expression_dataset.R
11 --data_source="$input.data_source"
12 #if $input.data_source == "immuno"
13 --hpa_ref="$__tool_directory__/normal_tissue.tsv"
14 --tissue="$input.normal_tissue"
15 --level="$input.level"
16 --reliability="$input.reliability"
17 #else if $input.data_source == "rnaseq"
18 --hpa_ref="$__tool_directory__/rna_tissue.tsv"
19 --sample="$input.sample"
20 #end if
21 --output="$output"
22 </command>
23
24 <inputs>
25 <conditional name="input">
26 <param name="data_source" type="select" label="Please choose experimental data source (antibody- or RNAseq-based)">
27 <option value="immuno">Expression profiles based on immunohistochemistry</option>
28 <option value="rnaseq">RNA levels based on RNA-seq</option>
29 </param>
30 <when value="immuno">
31 <param name="normal_tissue" type="select" label="Select tissue by clicking the dropdown menu below" multiple="True" optional="False">
32 <option value="adrenal gland" >Adrenal gland</option>
33 <option value="appendix" >Appendix</option>
34 <option value="bone marrow" >Bone marrow</option>
35 <option value="breast" >Breast</option>
36 <option value="bronchus" >Bronchus</option>
37 <option value="caudate" >Caudate</option>
38 <option value="cerebellum" >Cerebellum</option>
39 <option value="cerebral cortex" >Cerebral cortex</option>
40 <option value="cervix" >Cervix</option>
41 <option value="colon" >Colon</option>
42 <option value="duodenum" >Duodenum</option>
43 <option value="endometrium 1" >Endometrium 1</option>
44 <option value="endometrium 2" >Endometrium 2</option>
45 <option value="epididymis" >Epididymis</option>
46 <option value="esophagus" >Esophagus</option>
47 <option value="fallopian tube" >Fallopian tube</option>
48 <option value="gallbladder" >Gallbladder</option>
49 <option value="heart muscle" >Heart muscle</option>
50 <option value="hippocampus" >Hippocampus</option>
51 <option value="kidney" >Kidney</option>
52 <option value="liver" >Liver</option>
53 <option value="lung" >Lung</option>
54 <option value="lymph node" >Lymph node</option>
55 <option value="nasopharynx" >Nasopharynx</option>
56 <option value="oral mucosa" >Oral mucosa</option>
57 <option value="ovary" >Ovary</option>
58 <option value="pancreas" >Pancreas</option>
59 <option value="parathyroid gland" >Parathyroid gland</option>
60 <option value="placenta" >Placenta</option>
61 <option value="prostate" >Prostate</option>
62 <option value="rectum" >Rectum</option>
63 <option value="salivary gland" >Salivary gland</option>
64 <option value="seminal vesicle" >Seminal vesicle</option>
65 <option value="skeletal muscle" >Skeletal muscle</option>
66 <option value="skin 1" >Skin 1</option>
67 <option value="skin 2" >Skin 2</option>
68 <option value="small intestine" >Small intestine</option>
69 <option value="smooth muscle" >Smooth muscle</option>
70 <option value="soft tissue 1" >Soft tissue 1</option>
71 <option value="soft tissue 2" >Soft tissue 2</option>
72 <option value="spleen" >Spleen</option>
73 <option value="stomach 1" >Stomach 1</option>
74 <option value="stomach 2" >Stomach 2</option>
75 <option value="testis" >Testis</option>
76 <option value="thyroid gland" >Thyroid gland</option>
77 <option value="tonsil" >Tonsil</option>
78 <option value="urinary bladder" >Urinary bladder</option>
79 <option value="vagina" >Vagina</option>
80 </param>
81 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
82 <option value="High" selected="true">High</option>
83 <option value="Medium">Medium</option>
84 <option value="Low">Low</option>
85 <option value="Not detected">Not detected</option>
86 </param>
87 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
88 <option value="Enhanced" selected="true">Enhanced</option>
89 <option value="Supported" selected="true">Supported</option>
90 <option value="Approved">Approved</option>
91 <option value="Uncertain">Uncertain</option>
92
93 </param>
94 </when>
95 <when value="rnaseq">
96 <param name="sample" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" optional="False">
97 <option value="adipose tissue">Adipose tissue</option>
98 <option value="adrenal gland">Adrenal gland</option>
99 <option value="appendix">Appendix</option>
100 <option value="bone marrow">Bone marrow</option>
101 <option value="breast">Breast</option>
102 <option value="cerebral cortex">Cerebral cortex</option>
103 <option value="cervix, uterine">Cervix, uterine</option>
104 <option value="colon">Colon</option>
105 <option value="duodenum">Duodenum</option>
106 <option value="endometrium">Endometrium</option>
107 <option value="epididymis">Epididymis</option>
108 <option value="esophagus">Esophagus</option>
109 <option value="fallopian tube">Fallopian tube</option>
110 <option value="gallbladder">Gallbladder</option>
111 <option value="heart muscle">Heart muscle</option>
112 <option value="kidney">Kidney</option>
113 <option value="liver">Liver</option>
114 <option value="lung">Lung</option>
115 <option value="lymph node">Lymph node</option>
116 <option value="ovary">Ovary</option>
117 <option value="pancreas">Pancreas</option>
118 <option value="parathyroid gland">Parathyroid gland</option>
119 <option value="placenta">Placenta</option>
120 <option value="prostate">Prostate</option>
121 <option value="rectum">Rectum</option>
122 <option value="salivary gland">Salivary gland</option>
123 <option value="seminal vesicle">Seminal vesicle</option>
124 <option value="skeletal muscle">Skeletal muscle</option>
125 <option value="skin">Skin</option>
126 <option value="small intestine">Small intestine</option>
127 <option value="smooth muscle">Smooth muscle</option>
128 <option value="spleen">Spleen</option>
129 <option value="stomach">Stomach</option>
130 <option value="testis">Testis</option>
131 <option value="thyroid gland">Thyroid gland</option>
132 <option value="tonsil">Tonsil</option>
133 <option value="rinary bladder">Urinary bladder</option>
134 </param>
135 </when>
136 </conditional>
137 </inputs>
138
139 <outputs>
140 <data name="output" format="tsv" label=""/>
141 </outputs>
142
143 <tests>
144 <test>
145 <conditional name="input">
146 <param name="data_source" value="immuno"/>
147 <param name="normal_tissue" value="lung,ovary"/>
148 <param name="level" value="High"/>
149 <param name="reliability" value="Approved,Supported"/>
150 </conditional>
151 <output name="output" file="test.txt"/>
152 </test>
153 </tests>
154
155 <help><![CDATA[
156
157 This tool allows to retrieve information from Human Protein Atlas (https://www.proteinatlas.org/)
158 regarding the expression profiles of human genes both at the mRNA and protein levels
159 without any input required. It could be used to:
160
161 * Select a list of proteins highly expressed in a given tissue for data mining or comparison purpose in terms of expected protein content from one tissue to another
162
163 * Build a "reference" proteome restricted to a given tissue (for instance for GO analysis as a reference background restricted to a biological sample)
164
165 The resources from Human Protein Atlas that can be queried are the following:
166
167 1. Human normal tissue data: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays measured in 58 tissues and 82 cell types.
168
169 The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability score").
170
171 The reliability score is divided into Enhanced, Supported, Approved, or Uncertain with the following definitions:
172
173 * Enhanced: One or several antibodies with non-overlapping epitopes targeting the same gene have obtained enhanced validation based on orthogonal or independent antibody validation method.
174
175 * Supported: Consistency with RNA-seq and/or protein/gene characterization data, in combination with similar staining pattern if independent antibodies are available.
176
177 * Approved: Consistency with RNA-seq data in combination with inconsistency with, or lack of, protein/gene characterization data. Alternatively, consistency with protein/gene characterization data in combination with inconsistency with RNA-seq data. If independent antibodies are available, the staining pattern is partly similar or dissimilar.
178
179 * Uncertain:
180
181 Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, in combination with dissimilar staining pattern if independent antibodies are available.
182
183 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
184
185 2. RNA levels based on RNA-seq data: RNA levels measured in 64 cell lines and 37 tissues based on RNA-seq experiments. The tab-separated file includes Ensembl gene identifier ("Gene"), analysed sample ("Sample") and transcripts per million ("Value" and "Unit").
186
187 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
188
189 For more information: https://www.proteinatlas.org/about/help
190
191 -----
192
193 .. class:: infomark
194
195 **Authors**
196
197 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
198
199 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
200
201 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
202
203 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
204
205 ]]></help>
206
207 <citations>
208 </citations>
209
210 </tool>