|
0
|
1 <tool id="glytools_get_CFG_cell" name="GAP Get CFG cell" version="0.3">
|
|
|
2
|
|
|
3 <description>download msa entries from CFG</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
|
|
|
6 </requirements>
|
|
|
7 <stdio>
|
|
|
8 <regex match="IOError"
|
|
|
9 source="both"
|
|
|
10 level="fatal"
|
|
|
11 description="IOError" />
|
|
|
12 <regex match="UserWarning: gzip transfer encoding is experimental"
|
|
|
13 source="both"
|
|
|
14 level="warning"
|
|
|
15 description="Warning re use of gzip encoding" />
|
|
|
16 <regex match="br.set_handle_gzip(True)"
|
|
|
17 source="both"
|
|
|
18 level="warning"
|
|
|
19 description="Warning re use of gzip encoding" />
|
|
|
20 <regex match="IOError"
|
|
|
21 source="both"
|
|
|
22 level="fatal"
|
|
|
23 description="IOError" />
|
|
|
24 </stdio>
|
|
|
25 <command interpreter="python"><![CDATA[ cfg_get_glycan_from_cells.py -s "$species" -p "$investigator" -g "$glycantype" -c "$celltype" -o "$html_file" --filepath "msa_output" ]]></command>
|
|
|
26 <inputs>
|
|
|
27 <param name="species" type="select" label="Species">
|
|
|
28 <option value="Chinese Hamster" selected="false">Chinese Hamster</option>
|
|
|
29 <option value="Human" selected="true">Human</option>
|
|
|
30 <option value="Mouse" selected="false">Mouse</option>
|
|
|
31 <option value="all" selected="false">all</option>
|
|
|
32 </param>
|
|
|
33 <param name="investigator" type="select" label="Investigator">
|
|
|
34 <option value="all" selected="true">all</option>
|
|
|
35 <option value="Agbandje-McKenna, Mavis" selected="false">
|
|
|
36 Agbandje-McKenna, Mavis
|
|
|
37 </option>
|
|
|
38 <option value="Appelmelk, Ben J. " selected="false">
|
|
|
39 Appelmelk, Ben J.
|
|
|
40 </option>
|
|
|
41 <option value="Bennett, Eric" selected="false">
|
|
|
42 Bennett, Eric
|
|
|
43 </option>
|
|
|
44 <option value="Bochner, Bruce S." selected="false">
|
|
|
45 Bochner, Bruce S.
|
|
|
46 </option>
|
|
|
47 <option value="Cheng, Pi-Wan" selected="false">
|
|
|
48 Cheng, Pi-Wan
|
|
|
49 </option>
|
|
|
50 <option value="Contag, Christopher" selected="false">
|
|
|
51 Contag, Christopher
|
|
|
52 </option>
|
|
|
53 <option value="Cook-Mills, Joan" selected="false">
|
|
|
54 Cook-Mills, Joan
|
|
|
55 </option>
|
|
|
56 <option value="Crocker,Paul" selected="false">
|
|
|
57 Crocker,Paul
|
|
|
58 </option>
|
|
|
59 <option value="Cummings,Richard D. " selected="false">
|
|
|
60 Cummings,Richard D.
|
|
|
61 </option>
|
|
|
62 <option value="Dennis, James W." selected="false">
|
|
|
63 Dennis, James W.
|
|
|
64 </option>
|
|
|
65 <option value="Dimitroff, Charles" selected="false">
|
|
|
66 Dimitroff, Charles
|
|
|
67 </option>
|
|
|
68 <option value="Gordon, Siamon" selected="false">
|
|
|
69 Gordon, Siamon
|
|
|
70 </option>
|
|
|
71 <option value="Henion, Timothy" selected="false">
|
|
|
72 Henion, Timothy
|
|
|
73 </option>
|
|
|
74 <option value="Jackson, David " selected="false">
|
|
|
75 Jackson, David
|
|
|
76 </option>
|
|
|
77 <option value="Jaye, David" selected="false">
|
|
|
78 Jaye, David
|
|
|
79 </option>
|
|
|
80 <option value="Liu, FuTong" selected="false">
|
|
|
81 Liu, FuTong
|
|
|
82 </option>
|
|
|
83 <option value="Mahal, Lara K." selected="false">
|
|
|
84 Mahal, Lara K.
|
|
|
85 </option>
|
|
|
86 <option value="Merrill, Alfred" selected="false">
|
|
|
87 Merrill, Alfred
|
|
|
88 </option>
|
|
|
89 <option value="Metcalfe, Dean D." selected="false">
|
|
|
90 Metcalfe, Dean D.
|
|
|
91 </option>
|
|
|
92 <option value="Nitschke, Lars" selected="false">
|
|
|
93 Nitschke, Lars
|
|
|
94 </option>
|
|
|
95 <option value="Panjwani, Noorjahan" selected="false">
|
|
|
96 Panjwani, Noorjahan
|
|
|
97 </option>
|
|
|
98 <option value="Paulson, Henry" selected="false">
|
|
|
99 Paulson, Henry
|
|
|
100 </option>
|
|
|
101 <option value="Paulson, James" selected="false">
|
|
|
102 Paulson, James
|
|
|
103 </option>
|
|
|
104 <option value="Rittenhouse-Olson, Kate" selected="false">
|
|
|
105 Rittenhouse-Olson, Kate
|
|
|
106 </option>
|
|
|
107 <option value="Romagne, Francois" selected="false">
|
|
|
108 Romagne, Francois
|
|
|
109 </option>
|
|
|
110 <option value="Salomon,Daniel " selected="false">
|
|
|
111 Salomon,Daniel
|
|
|
112 </option>
|
|
|
113 <option value="Stanley, Pamela" selected="false">
|
|
|
114 Stanley, Pamela
|
|
|
115 </option>
|
|
|
116 <option value="Van Kooyk, Yvette" selected="false">
|
|
|
117 Van Kooyk, Yvette
|
|
|
118 </option>
|
|
|
119 <option value="Wild, Martin K." selected="false">
|
|
|
120 Wild, Martin K.
|
|
|
121 </option>
|
|
|
122 <option value="Wu, Hui" selected="false">
|
|
|
123 Wu, Hui
|
|
|
124 </option>
|
|
|
125 </param>
|
|
|
126 <param name="glycantype" type="select" label="Glycan Type Analysed">
|
|
|
127 <option value="all" selected="true">all</option>
|
|
|
128 <option value="N-Linked" selected="false">
|
|
|
129 N-Linked
|
|
|
130 </option>
|
|
|
131 <option value="Non-Polar Glycolipids" selected="false">
|
|
|
132 Non-Polar Glycolipids
|
|
|
133 </option>
|
|
|
134 <option value="O-Linked" selected="false">
|
|
|
135 O-Linked
|
|
|
136 </option>
|
|
|
137 <option value="Polar Glycolipids" selected="false">
|
|
|
138 Polar Glycolipids
|
|
|
139 </option>
|
|
|
140 </param>
|
|
|
141 <param name="celltype" type="select" label="Cell Type">
|
|
|
142 <option value="all" selected="true">all</option>
|
|
|
143 <option value="A9 fibroblasts" selected="false">
|
|
|
144 A9 fibroblasts
|
|
|
145 </option>
|
|
|
146 <option value="Antibodies" selected="false">
|
|
|
147 Antibodies
|
|
|
148 </option>
|
|
|
149 <option value="B-Cells" selected="false">
|
|
|
150 B-Cells
|
|
|
151 </option>
|
|
|
152 <option value="B1 Cells" selected="false">
|
|
|
153 B1 Cells
|
|
|
154 </option>
|
|
|
155 <option value="Basophils" selected="false">
|
|
|
156 Basophils
|
|
|
157 </option>
|
|
|
158 <option value="Bone marrow mast cells (BMMC)" selected="false">
|
|
|
159 Bone marrow mast cells (BMMC)
|
|
|
160 </option>
|
|
|
161 <option value="CHO" selected="false">
|
|
|
162 CHO
|
|
|
163 </option>
|
|
|
164 <option value="CHO -Lec10.3C" selected="false">
|
|
|
165 CHO -Lec10.3C
|
|
|
166 </option>
|
|
|
167 <option value="CHO -Lec1.3C" selected="false">
|
|
|
168 CHO -Lec1.3C
|
|
|
169 </option>
|
|
|
170 <option value="CHO -Lec13.6A" selected="false">
|
|
|
171 CHO -Lec13.6A
|
|
|
172 </option>
|
|
|
173 <option value="CHO -Lec2.6A" selected="false">
|
|
|
174 CHO -Lec2.6A
|
|
|
175 </option>
|
|
|
176 <option value="CHO -Lec4.7B" selected="false">
|
|
|
177 CHO -Lec4.7B
|
|
|
178 </option>
|
|
|
179 <option value="CHO LEC11.E7" selected="false">
|
|
|
180 CHO LEC11.E7
|
|
|
181 </option>
|
|
|
182 <option value="CHO LEC12.1B" selected="false">
|
|
|
183 CHO LEC12.1B
|
|
|
184 </option>
|
|
|
185 <option value="CHO LEC14.4A" selected="false">
|
|
|
186 CHO LEC14.4A
|
|
|
187 </option>
|
|
|
188 <option value="CHO LEC18.21B" selected="false">
|
|
|
189 CHO LEC18.21B
|
|
|
190 </option>
|
|
|
191 <option value="CHO LEC30.H2" selected="false">
|
|
|
192 CHO LEC30.H2
|
|
|
193 </option>
|
|
|
194 <option value="Cytokine-induced killer (CIK) cells" selected="false">
|
|
|
195 Cytokine-induced killer (CIK) cells
|
|
|
196 </option>
|
|
|
197 <option value="Dendritic Cells" selected="false">
|
|
|
198 Dendritic Cells
|
|
|
199 </option>
|
|
|
200 <option value="EL4 T lymphocytes" selected="false">
|
|
|
201 EL4 T lymphocytes
|
|
|
202 </option>
|
|
|
203 <option value="Eosinophils " selected="false">
|
|
|
204 Eosinophils
|
|
|
205 </option>
|
|
|
206 <option value="Erythrocytes" selected="false">
|
|
|
207 Erythrocytes
|
|
|
208 </option>
|
|
|
209 <option value="HL-60" selected="false">
|
|
|
210 HL-60
|
|
|
211 </option>
|
|
|
212 <option value="HeLa EV2" selected="false">
|
|
|
213 HeLa EV2
|
|
|
214 </option>
|
|
|
215 <option value="HeLa PF" selected="false">
|
|
|
216 HeLa PF
|
|
|
217 </option>
|
|
|
218 <option value="Human Dermal Lymphatic Endothelial Cells (HDLEC) " selected="false">
|
|
|
219 Human Dermal Lymphatic Endothelial Cells (HDLEC)
|
|
|
220 </option>
|
|
|
221 <option value="Human Prostate LNCaP Cells " selected="false">
|
|
|
222 Human Prostate LNCaP Cells
|
|
|
223 </option>
|
|
|
224 <option value="Immunoglobulin (Plasma extract) " selected="false">
|
|
|
225 Immunoglobulin (Plasma extract)
|
|
|
226 </option>
|
|
|
227 <option value="K562" selected="false">
|
|
|
228 K562
|
|
|
229 </option>
|
|
|
230 <option value="KG-1a" selected="false">
|
|
|
231 KG-1a
|
|
|
232 </option>
|
|
|
233 <option value="KG1a Cells" selected="false">
|
|
|
234 KG1a Cells
|
|
|
235 </option>
|
|
|
236 <option value="Macrophages" selected="false">
|
|
|
237 Macrophages
|
|
|
238 </option>
|
|
|
239 <option value="Mast Cells" selected="false">
|
|
|
240 Mast Cells
|
|
|
241 </option>
|
|
|
242 <option value="Monocytes" selected="false">
|
|
|
243 Monocytes
|
|
|
244 </option>
|
|
|
245 <option value="Murine mammary carcinoma" selected="false">
|
|
|
246 Murine mammary carcinoma
|
|
|
247 </option>
|
|
|
248 <option value="Natural Killer Cells" selected="false">
|
|
|
249 Natural Killer Cells
|
|
|
250 </option>
|
|
|
251 <option value="Natural killer cells" selected="false">
|
|
|
252 Natural killer cells
|
|
|
253 </option>
|
|
|
254 <option value="Neurons" selected="false">
|
|
|
255 Neurons
|
|
|
256 </option>
|
|
|
257 <option value="Neutrophils" selected="false">
|
|
|
258 Neutrophils
|
|
|
259 </option>
|
|
|
260 <option value="Osteoclasts" selected="false">
|
|
|
261 Osteoclasts
|
|
|
262 </option>
|
|
|
263 <option value="Peripheral Blood Mononuclear Cells (PBMC)" selected="false">
|
|
|
264 Peripheral Blood Mononuclear Cells (PBMC)
|
|
|
265 </option>
|
|
|
266 <option value="RAW" selected="false">
|
|
|
267 RAW
|
|
|
268 </option>
|
|
|
269 <option value="RAW 264.7 Cells" selected="false">
|
|
|
270 RAW 264.7 Cells
|
|
|
271 </option>
|
|
|
272 <option value="SV40 transformed fibroblast cell line, NB324K" selected="false">
|
|
|
273 SV40 transformed fibroblast cell line, NB324K
|
|
|
274 </option>
|
|
|
275 <option value="T-Cells" selected="false">
|
|
|
276 T-Cells
|
|
|
277 </option>
|
|
|
278 <option value="THP-1" selected="false">
|
|
|
279 THP-1
|
|
|
280 </option>
|
|
|
281 <option value="VG37" selected="false">
|
|
|
282 VG37
|
|
|
283 </option>
|
|
|
284 <option value="WEHI 231 B Cells" selected="false">
|
|
|
285 WEHI 231 B Cells
|
|
|
286 </option>
|
|
|
287 <option value="WEHI-3" selected="false">
|
|
|
288 WEHI-3
|
|
|
289 </option>
|
|
|
290 </param>
|
|
|
291 </inputs>
|
|
|
292 <outputs>
|
|
|
293 <data format="html" name="html_file" label="Summary_${tool.name}.html">
|
|
|
294 <discover_datasets pattern="__designation_and_ext__" directory="msa_output" visible="true" />
|
|
|
295 </data>
|
|
|
296 </outputs>
|
|
|
297 <help> <![CDATA[
|
|
|
298 .. class:: infomark
|
|
|
299
|
|
|
300 **What this tool does**
|
|
|
301
|
|
|
302 This tool will request Annotated Mass spec (msa) data from the Consortium for Functional Glycomics.
|
|
|
303
|
|
|
304 .. class:: infomark
|
|
|
305
|
|
|
306 **Input**
|
|
|
307
|
|
|
308 Your choice of Species, Participating Investigator, Glycan type and Cell type as per the CFG request page.
|
|
|
309
|
|
|
310 ----
|
|
|
311
|
|
|
312 .. class:: infomark
|
|
|
313
|
|
|
314 **Output**
|
|
|
315
|
|
|
316 HTML summary of retrieved information (Note links in html do not function within Galaxy).
|
|
|
317
|
|
|
318 A number of autodiscovered msa datasets (refresh browser if necessary).
|
|
|
319
|
|
|
320
|
|
|
321 ]]>
|
|
|
322 </help>
|
|
|
323
|
|
|
324 </tool>
|
