Mercurial > repos > proteore > proteore_expression_levels_by_tissue

comparison get_expression_profiles.xml @ 12:56c93d1fc8fd draft

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planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:10:08 -0400
parents 6e85f07c20ee
children 2173192d4824
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1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.13"> 1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.06.27">
2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas] 2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
36 --not_mapped="$not_mapped" 36 --not_mapped="$not_mapped"
37 --output="$hpa_output" 37 --output="$hpa_output"
38 </command> 38 </command>
39 <inputs> 39 <inputs>
40 <conditional name="input" > 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)" > 41 <param name="ids" type="select" label="Enter your IDs (Ensembl gene ID only; e.g. ENSG00000163631)" help="Copy/paste or from a file (e.g. table)" >
42 <option value="list">Copy/paste your IDs</option> 42 <option value="list">Copy/paste your IDs</option>
43 <option value="file" selected="true">Input file containing your IDs</option> 43 <option value="file" selected="true">Input file containing your IDs</option>
44 </param> 44 </param>
45 <when value="list" > 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' > 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' >
66 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)"> 66 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)">
67 <option value="normal">Human Normal Tissue</option> 67 <option value="normal">Human Normal Tissue</option>
68 <option value="tumor">Human Tumor Tissue</option> 68 <option value="tumor">Human Tumor Tissue</option>
69 </param> 69 </param>
70 <when value="normal"> 70 <when value="normal">
71 <param name="proteinatlas" type="select" label="Normal tissue HPA version" > 71 <param name="proteinatlas" type="select" label="Normal tissue HPA version 18.1" >
72 <options from_data_table="proteore_protein_atlas_normal_tissue"/> 72 <options from_data_table="proteore_protein_atlas_normal_tissue">
73 <filter type="sort_by" column="0"/>
74 </options>
73 </param> 75 </param>
74 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> 76 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
75 <option value="adrenal gland" >Adrenal gland</option> 77 <option value="adrenal gland" >Adrenal gland</option>
76 <option value="appendix" >Appendix</option> 78 <option value="appendix" >Appendix</option>
77 <option value="bone marrow" >Bone marrow</option> 79 <option value="bone marrow" >Bone marrow</option>
121 <option value="urinary bladder" >Urinary bladder</option> 123 <option value="urinary bladder" >Urinary bladder</option>
122 <option value="vagina" >Vagina</option> 124 <option value="vagina" >Vagina</option>
123 </param> 125 </param>
124 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False"> 126 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
125 <option value="High" selected="true">High</option> 127 <option value="High" selected="true">High</option>
126 <option value="Medium">Medium</option> 128 <option value="Medium" selected="true">Medium</option>
127 <option value="Low">Low</option> 129 <option value="Low">Low</option>
128 <option value="Not detected">Not detected</option> 130 <option value="Not detected">Not detected</option>
129 </param> 131 </param>
130 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False"> 132 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
131 <option value="Enhanced" selected="true">Enhanced</option> 133 <option value="Enhanced" selected="true">Enhanced</option>
133 <option value="Approved">Approved</option> 135 <option value="Approved">Approved</option>
134 <option value="Uncertain">Uncertain</option> 136 <option value="Uncertain">Uncertain</option>
135 </param> 137 </param>
136 </when> 138 </when>
137 <when value="tumor"> 139 <when value="tumor">
138 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > 140 <param name="proteinatlas" type="select" label="Tumor tissue HPA version 18.1" >
139 <options from_data_table="proteore_protein_atlas_tumor_tissue"/> 141 <options from_data_table="proteore_protein_atlas_tumor_tissue">
142 <filter type="sort_by" column="0"/>
143 </options>
140 </param> 144 </param>
141 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False"> 145 <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> 146 <option value="breast cancer" >Breast cancer</option>
143 <option value="carcinoid" >Carcinoid</option> 147 <option value="carcinoid" >Carcinoid</option>
144 <option value="cervical cancer" >Cervical cancer</option> 148 <option value="cervical cancer" >Cervical cancer</option>
192 196
193 This tool allows to retrieve expression profiles (normal or tumor tissue) from Human Protein Atlas (https://www.proteinatlas.org/) 197 This tool allows to retrieve expression profiles (normal or tumor tissue) from Human Protein Atlas (https://www.proteinatlas.org/)
194 198
195 **Input** 199 **Input**
196 200
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. 201 A list of Ensembl gene IDs (e.g. ENSG00000163631) 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.
202
203 A line can contains multiple ids if separated by ";".
204
205 .. class:: warningmark
206
207 In copy/paste mode, the number of IDs considered in input is limited to 5000.
198 208
199 ----- 209 -----
200 210
201 **Parameters** 211 **Parameters**
202 212
230 240
231 ----- 241 -----
232 242
233 **Data sources (release date)** 243 **Data sources (release date)**
234 244
235 Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38. 245 Both normal and tumor tissues data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38. More information: https://www.proteinatlas.org/about/download
236 246
237 ----- 247 -----
238 248
239 .. class:: infomark 249 .. class:: infomark
240 250
244 254
245 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 255 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
246 256
247 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 257 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
248 258
249 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 259 Help: contact@proteore.org for any questions or concerns about this tool.
250 260
251 ]]></help> 261 ]]></help>
252 <citations> 262 <citations>
253 </citations> 263 </citations>
254 </tool> 264 </tool>