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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:14:10 -0400
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6:1c3a5ceab3cd 7:6a9db2cc54de
1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.05.17"> 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"/> 73 <filter type="sort_by" column="0"/>
74 </options> 74 </options>
75 </param> 75 </param>
76 <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">
123 <option value="urinary bladder" >Urinary bladder</option> 123 <option value="urinary bladder" >Urinary bladder</option>
124 <option value="vagina" >Vagina</option> 124 <option value="vagina" >Vagina</option>
125 </param> 125 </param>
126 <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">
127 <option value="High" selected="true">High</option> 127 <option value="High" selected="true">High</option>
128 <option value="Medium">Medium</option> 128 <option value="Medium" selected="true">Medium</option>
129 <option value="Low">Low</option> 129 <option value="Low">Low</option>
130 <option value="Not detected">Not detected</option> 130 <option value="Not detected">Not detected</option>
131 </param> 131 </param>
132 <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">
133 <option value="Enhanced" selected="true">Enhanced</option> 133 <option value="Enhanced" selected="true">Enhanced</option>
135 <option value="Approved">Approved</option> 135 <option value="Approved">Approved</option>
136 <option value="Uncertain">Uncertain</option> 136 <option value="Uncertain">Uncertain</option>
137 </param> 137 </param>
138 </when> 138 </when>
139 <when value="tumor"> 139 <when value="tumor">
140 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > 140 <param name="proteinatlas" type="select" label="Tumor tissue HPA version 18.1" >
141 <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"/> 142 <filter type="sort_by" column="0"/>
143 </options> 143 </options>
144 </param> 144 </param>
145 <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">
196 196
197 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/)
198 198
199 **Input** 199 **Input**
200 200
201 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.
202 202
203 A line can contains multiple ids if separated by ";". 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.
204 208
205 ----- 209 -----
206 210
207 **Parameters** 211 **Parameters**
208 212
236 240
237 ----- 241 -----
238 242
239 **Data sources (release date)** 243 **Data sources (release date)**
240 244
241 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
242 246
243 ----- 247 -----
244 248
245 .. class:: infomark 249 .. class:: infomark
246 250
250 254
251 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
252 256
253 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.
254 258
255 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.
256 260
257 ]]></help> 261 ]]></help>
258 <citations> 262 <citations>
259 </citations> 263 </citations>
260 </tool> 264 </tool>