Mercurial > repos > proteore > proteore_expression_levels_by_tissue

comparison get_expression_profiles.xml @ 3:3bedd074c485 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c6e1fd1f68e81ce9eea6ad66adee21070f2893ef-dirty
author proteore
date Wed, 06 Mar 2019 09:19:05 -0500
parents
children 5cd79aa7aac9
comparison
equal deleted inserted replaced
2:db2cd451835f 3:3bedd074c485
1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.06">
2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas]
3 </description>
4 <requirements>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command interpreter="Rscript">
10 $__tool_directory__/get_expression_profiles.R
11
12 #if "protein_atlas" in str($options.proteinatlas).split("/")
13 --ref_file="$options.proteinatlas"
14 #else
15 --ref_file="$__tool_directory__/$options.proteinatlas"
16 #end if
17
18 --input_type="$input.ids"
19 #if $input.ids == "list"
20 --input="$input.list"
21 #else
22 --input="$input.file"
23 --column_number="$input.ncol"
24 --header="$input.header"
25 #end if
26
27 #if $options.database == "normal"
28 --atlas="normal"
29 --tissue="$options.normal_tissue"
30 --level="$options.level"
31 --reliability="$options.reliability"
32 #else if $options.database == "tumor"
33 --atlas="cancer"
34 --cancer="$options.cancer_tissue"
35 #end if
36 --not_mapped="$not_mapped"
37 --output="$hpa_output"
38 </command>
39 <inputs>
40 <conditional name="input" >
41 <param name="ids" type="select" label="Enter your IDs (ENSG IDs only)" help="Copy/paste or from a file (e.g. table)" >
42 <option value="list">Copy/paste your IDs</option>
43 <option value="file" selected="true">Input file containing your IDs</option>
44 </param>
45 <when value="list" >
46 <param name="list" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: ENSG00000174876 ENSG00000178372 ENSG00000159763' >
47 <sanitizer>
48 <valid initial="string.printable">
49 <remove value="&apos;"/>
50 </valid>
51 <mapping initial="none">
52 <add source="&apos;" target="__sq__"/>
53 </mapping>
54 </sanitizer>
55 </param>
56 </when>
57 <when value="file" >
58 <param name="file" type="data" format="txt,tabular" label="" help="" />
59 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
60 <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
61 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
62 </param>
63 </when>
64 </conditional>
65 <conditional name="options">
66 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)">
67 <option value="normal">Human Normal Tissue</option>
68 <option value="tumor">Human Tumor Tissue</option>
69 </param>
70 <when value="normal">
71 <param name="proteinatlas" type="select" label="Normal tissue HPA version" >
72 <options from_data_table="proteore_protein_atlas_normal_tissue"/>
73 </param>
74 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
75 <option value="adrenal gland" >Adrenal gland</option>
76 <option value="appendix" >Appendix</option>
77 <option value="bone marrow" >Bone marrow</option>
78 <option value="breast" >Breast</option>
79 <option value="bronchus" >Bronchus</option>
80 <option value="caudate" >Caudate</option>
81 <option value="cerebellum" >Cerebellum</option>
82 <option value="cerebral cortex" >Cerebral cortex</option>
83 <option value="cervix" >Cervix</option>
84 <option value="colon" >Colon</option>
85 <option value="duodenum" >Duodenum</option>
86 <option value="endometrium 1" >Endometrium 1</option>
87 <option value="endometrium 2" >Endometrium 2</option>
88 <option value="epididymis" >Epididymis</option>
89 <option value="esophagus" >Esophagus</option>
90 <option value="fallopian tube" >Fallopian tube</option>
91 <option value="gallbladder" >Gallbladder</option>
92 <option value="heart muscle" >Heart muscle</option>
93 <option value="hippocampus" >Hippocampus</option>
94 <option value="kidney" >Kidney</option>
95 <option value="liver" >Liver</option>
96 <option value="lung" >Lung</option>
97 <option value="lymph node" >Lymph node</option>
98 <option value="nasopharynx" >Nasopharynx</option>
99 <option value="oral mucosa" >Oral mucosa</option>
100 <option value="ovary" >Ovary</option>
101 <option value="pancreas" >Pancreas</option>
102 <option value="parathyroid gland" >Parathyroid gland</option>
103 <option value="placenta" >Placenta</option>
104 <option value="prostate" >Prostate</option>
105 <option value="rectum" >Rectum</option>
106 <option value="salivary gland" >Salivary gland</option>
107 <option value="seminal vesicle" >Seminal vesicle</option>
108 <option value="skeletal muscle" >Skeletal muscle</option>
109 <option value="skin 1" >Skin 1</option>
110 <option value="skin 2" >Skin 2</option>
111 <option value="small intestine" >Small intestine</option>
112 <option value="smooth muscle" >Smooth muscle</option>
113 <option value="soft tissue 1" >Soft tissue 1</option>
114 <option value="soft tissue 2" >Soft tissue 2</option>
115 <option value="spleen" >Spleen</option>
116 <option value="stomach 1" >Stomach 1</option>
117 <option value="stomach 2" >Stomach 2</option>
118 <option value="testis" >Testis</option>
119 <option value="thyroid gland" >Thyroid gland</option>
120 <option value="tonsil" >Tonsil</option>
121 <option value="urinary bladder" >Urinary bladder</option>
122 <option value="vagina" >Vagina</option>
123 </param>
124 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
125 <option value="High" selected="true">High</option>
126 <option value="Medium">Medium</option>
127 <option value="Low">Low</option>
128 <option value="Not detected">Not detected</option>
129 </param>
130 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
131 <option value="Enhanced" selected="true">Enhanced</option>
132 <option value="Supported" selected="true">Supported</option>
133 <option value="Approved">Approved</option>
134 <option value="Uncertain">Uncertain</option>
135 </param>
136 </when>
137 <when value="tumor">
138 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" >
139 <options from_data_table="proteore_protein_atlas_tumor_tissue"/>
140 </param>
141 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False">
142 <option value="breast cancer" >Breast cancer</option>
143 <option value="carcinoid" >Carcinoid</option>
144 <option value="cervical cancer" >Cervical cancer</option>
145 <option value="colorectal cancer" >Colorectal cancer</option>
146 <option value="endometrial cancer" >Endometrial cancer</option>
147 <option value="glioma" >Glioma</option>
148 <option value="head and neck cancer" >Head and neck cancer</option>
149 <option value="liver cancer" >Liver cancer</option>
150 <option value="lung cancer" >Lung cancer</option>
151 <option value="lymphoma" >Lymphoma</option>
152 <option value="melanoma" >Melanoma</option>
153 <option value="ovarian cancer" >Ovarian cancer</option>
154 <option value="pancreatic cancer" >Pancreatic cancer</option>
155 <option value="prostate cancer" >Prostate cancer</option>
156 <option value="renal cancer" >Renal cancer</option>
157 <option value="skin cancer" >Skin cancer</option>
158 <option value="stomach cancer" >Stomach cancer</option>
159 <option value="testis cancer" >Testis cancer</option>
160 <option value="thyroid cancer" >Thyroid cancer</option>
161 <option value="urothelial cancer" >Urothelial cancer</option>
162 </param>
163 </when>
164 </conditional>
165 <param name="not_mapped" type="boolean" truevalue="true" falsevalue="false" label="Keep IDs not found in HPA?" checked="true"/>
166 </inputs>
167 <outputs>
168 <data name="hpa_output" format="tsv" label="" />
169 </outputs>
170 <tests>
171 <test>
172 <conditional name="input">
173 <param name="ids" value="file"/>
174 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
175 <param name="header" value="true"/>
176 <param name="ncol" value="c8"/>
177 </conditional>
178 <conditional name="options">
179 <param name="database" value="normal"/>
180 <param name="proteinatlas" value="normal_tissue.tsv"/>
181 <param name="normal_tissue" value="bronchus,lung,nasopharynx,salivary gland"/>
182 <param name="level" value="Not detected,Medium,High,Low"/>
183 <param name="reliability" value="Approved,Supported,Uncertain"/>
184 </conditional>
185 <param name="not_mapped" value="true" />
186 <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/>
187 </test>
188 </tests>
189 <help><![CDATA[
190
191 **Description**
192
193 This tool allows to retrieve expression profiles (normal or tumor tissue) from Human Protein Atlas (https://www.proteinatlas.org/)
194
195 **Input**
196
197 A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file); if it's not the case, please use the ID_Converter tool of ProteoRE.
198
199 -----
200
201 **Parameters**
202
203 "Human Protein Atlas (normal or tumor tissue)": two resources are currently available
204
205 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays.
206
207 **Output** will be in the form: a 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").
208
209 * **Human tumor tissue data**: staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays and log-rank P value for Kaplan-Meier analysis of correlation between mRNA expression level and patient survival.
210
211 **Ouptut** will be in the form: The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable").
212
213 "Select tissue(s)": information from more than one tissue can be retrieved
214
215 "Keep IDs not found in HPA?": ENSG ID not found in Human Protein Atlas will be returned in the output file in the form of "NA" (default is "No")
216
217 -----
218
219 **Reliability score (only for normal tissue)**
220
221 Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect to the definitions from HPA:
222
223 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.
224
225 Supported - Consistency with RNA-seq and/or protein/gene characterization data, in combination with similar staining pattern if independent antibodies are available.
226
227 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.
228
229 Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, in combination with dissimilar staining pattern if independent antibodies are available.
230
231 -----
232
233 **Data sources (release date)**
234
235 Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38.
236
237 -----
238
239 .. class:: infomark
240
241 **Authors**
242
243 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
244
245 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
246
247 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
248
249 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
250
251 ]]></help>
252 <citations>
253 </citations>
254 </tool>