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comparison get_data/cfg/getcfgcells.xml @ 0:89592faa2875 draft

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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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>