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comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_38.xml~ @ 0:049760c677de default tip

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Galaxy WSExtensions added successfully
author uga-galaxy-group
date Tue, 05 Jul 2011 19:34:18 -0400
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1 <tool id="client_38" name="genesbygenetype ">
2 <description> Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl </description>
3 <command interpreter="python">
4 client_1.py
5 #if $cond_source.optional_param_source=="no":
6 $output
7 $servicetype
8 $url
9 $method
10 http://eupathdb.org/webservices/GeneQuestions
11 organism
12 #if $source0.source0_source=="user":
13 $source0.user_param0
14 #else:
15 fileInput
16 $source0.cached_param0
17 #end if
18 includePseudogenes
19 #if $source1.source1_source=="user":
20 $source1.user_param1
21 #else:
22 fileInput
23 $source1.cached_param1
24 #end if
25 geneType
26 #if $source2.source2_source=="user":
27 $source2.user_param2
28 #else:
29 fileInput
30 $source2.cached_param2
31 #end if
32 #else:
33 $output
34 $servicetype
35 $url
36 $method
37 http://eupathdb.org/webservices/GeneQuestions
38 organism
39 #if $source0.source0_source=="user":
40 $source0.user_param0
41 #else:
42 fileInput
43 $source0.cached_param0
44 #end if
45 includePseudogenes
46 #if $source1.source1_source=="user":
47 $source1.user_param1
48 #else:
49 fileInput
50 $source1.cached_param1
51 #end if
52 geneType
53 #if $source2.source2_source=="user":
54 $source2.user_param2
55 #else:
56 fileInput
57 $source2.cached_param2
58 #end if
59 o-fields
60 #if $cond_source.source3.source3_source=="user":
61 $cond_source.source3.user_param3
62 #else:
63 fileInput
64 $cond_source.source3.cached_param3
65 #end if
66 o-tables
67 #if $cond_source.source4.source4_source=="user":
68 $cond_source.source4.user_param4
69 #else:
70 fileInput
71 $cond_source.source4.cached_param4
72 #end if
73 #end if
74 </command>
75 <inputs>
76 <param name="servicetype" type="hidden" value="REST"/>
77 <param name="url" type="hidden" value="http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl" />
78 <param name="method" type="hidden" value="http://eupathdb.org/webservices/GeneQuestions" />
79 <conditional name="source0">
80 <param name="source0_source" type="select" label="Organism Source">
81 <option value="cached" selected="true">Param value will be taken from previous step</option>
82 <option value="user">User will enter the param value</option>
83 </param>
84 <when value="user">
85 <param name="user_param0" type="select" label="Select Organism" help="see tip below">
86 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
87 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
88 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
89 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
90 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
91 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
92 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
93 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
94 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
95 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
96 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
97 <option value="Enterocytozoon**bieneusi" >Enterocytozoon bieneusi</option>
98 <option value="Babesia**bovis" >Babesia bovis</option>
99 <option value="Theileria**annulata" >Theileria annulata</option>
100 <option value="Theileria**parva" >Theileria parva</option>
101 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
102 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
103 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
104 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
105 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
106 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
107 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
108 <option value="Neospora**caninum" >Neospora caninum</option>
109 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
110 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
111 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
112 <option value="Leishmania**infantum" >Leishmania infantum</option>
113 <option value="Leishmania**major" >Leishmania major</option>
114 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
115 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
116 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
117 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
118 </param>
119 </when>
120 <when value="cached">
121 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/>
122 </when></conditional><conditional name="source1">
123 <param name="source1_source" type="select" label="Include Pseudogenes Source">
124 <option value="cached" selected="true">Param value will be taken from previous step</option>
125 <option value="user">User will enter the param value</option>
126 </param>
127 <when value="user">
128 <param name="user_param1" type="select" label="Select Include Pseudogenes" help="see tip below">
129 <option value="No" selected="true">No</option>
130 <option value="Yes" >Yes</option>
131 <option value="Pseudogenes**Only" >Pseudogenes Only</option>
132 </param>
133 </when>
134 <when value="cached">
135 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Include Pseudogenes"/>
136 </when></conditional><conditional name="source2">
137 <param name="source2_source" type="select" label="Gene type Source">
138 <option value="cached" selected="true">Param value will be taken from previous step</option>
139 <option value="user">User will enter the param value</option>
140 </param>
141 <when value="user">
142 <param name="user_param2" type="select" label="Select Gene type" help="see tip below">
143 <option value="protein**coding" selected="true">protein coding</option>
144 <option value="snRNA**encoding" >snRNA encoding</option>
145 <option value="tRNA**encoding" >tRNA encoding</option>
146 <option value="rRNA**encoding" >rRNA encoding</option>
147 <option value="misc**RNA" >misc RNA</option>
148 <option value="snoRNA**encoding" >snoRNA encoding</option>
149 <option value="SRP**RNA**encoding" >SRP RNA encoding</option>
150 <option value="RNase**P**RNA" >RNase P RNA</option>
151 <option value="RNase**MRP**RNA" >RNase MRP RNA</option>
152 <option value="repeat**region" >repeat region</option>
153 <option value="scRNA**encoding" >scRNA encoding</option>
154 </param>
155 </when>
156 <when value="cached">
157 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Gene type"/>
158 </when></conditional> <conditional name="cond_source">
159 <param name="optional_param_source" type="select" label="Display Additional Parameters">
160 <option value="no" selected="true">no</option>
161 <option value="yes">yes</option>
162 </param>
163 <when value="no">
164 </when>
165 <when value="yes">
166
167 <conditional name="source3">
168 <param name="source3_source" type="select" label="Output Fields Source">
169 <option value="cached" selected="true">Param value will be taken from previous step</option>
170 <option value="user">User will enter the param value</option>
171 </param>
172 <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
173 <option value="all" >all</option>
174 <option value="none" selected="true">none</option>
175 <option value="primary_key" >primary_key</option>
176 <option value="formatted_gene_id" >formatted_gene_id</option>
177 <option value="sequence_id" >sequence_id</option>
178 <option value="chromosome" >chromosome</option>
179 <option value="chromosome_order_num" >chromosome_order_num</option>
180 <option value="location_text" >location_text</option>
181 <option value="strand" >strand</option>
182 <option value="gene_type" >gene_type</option>
183 <option value="exon_count" >exon_count</option>
184 <option value="transcript_length" >transcript_length</option>
185 <option value="cds_length" >cds_length</option>
186 <option value="product" >product</option>
187 <option value="protein_length" >protein_length</option>
188 <option value="tm_count" >tm_count</option>
189 <option value="molecular_weight" >molecular_weight</option>
190 <option value="isoelectric_point" >isoelectric_point</option>
191 <option value="ec_numbers_string" >ec_numbers_string</option>
192 <option value="ortholog_number" >ortholog_number</option>
193 <option value="paralog_number" >paralog_number</option>
194 <option value="orthomcl_name" >orthomcl_name</option>
195 <option value="signalp_scores" >signalp_scores</option>
196 <option value="signalp_peptide" >signalp_peptide</option>
197 <option value="ann_go_function" >ann_go_function</option>
198 <option value="ann_go_process" >ann_go_process</option>
199 <option value="ann_go_component" >ann_go_component</option>
200 <option value="pred_go_function" >pred_go_function</option>
201 <option value="pred_go_process" >pred_go_process</option>
202 <option value="pred_go_component" >pred_go_component</option>
203 <option value="organism" >organism</option>
204 <option value="is_pseudo" >is_pseudo</option>
205 <option value="protein_sequence" >protein_sequence</option>
206 <option value="transcript_sequence" >transcript_sequence</option>
207 <option value="cds" >cds</option>
208 <option value="wdk_weight" >wdk_weight</option>
209 </param>
210 </when>
211 <when value="cached">
212 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/>
213 </when></conditional>
214
215 <conditional name="source4">
216 <param name="source4_source" type="select" label="Output Tables Source">
217 <option value="cached" selected="true">Param value will be taken from previous step</option>
218 <option value="user">User will enter the param value</option>
219 </param>
220 <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
221 <option value="all" >all</option>
222 <option value="none" selected="true">none</option>
223 <option value="SNPs" >SNPs</option>
224 <option value="GeneModelDump" >GeneModelDump</option>
225 <option value="InterPro" >InterPro</option>
226 <option value="TMHMM" >TMHMM</option>
227 <option value="LowComplexity" >LowComplexity</option>
228 <option value="SignalP" >SignalP</option>
229 <option value="BlastP" >BlastP</option>
230 <option value="Genbank" >Genbank</option>
231 <option value="SageTags" >SageTags</option>
232 <option value="Notes" >Notes</option>
233 <option value="UserComments" >UserComments</option>
234 <option value="CommunityExpComments" >CommunityExpComments</option>
235 <option value="EcNumber" >EcNumber</option>
236 <option value="MassSpec" >MassSpec</option>
237 <option value="GoTerms" >GoTerms</option>
238 <option value="Phenotype" >Phenotype</option>
239 <option value="Y2hInteractions" >Y2hInteractions</option>
240 <option value="Orthologs" >Orthologs</option>
241 <option value="MetabolicPathways" >MetabolicPathways</option>
242 <option value="TaskComments" >TaskComments</option>
243 <option value="ArrayElements" >ArrayElements</option>
244 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
245 <option value="ProteinExpression" >ProteinExpression</option>
246 <option value="Mr4Reagents" >Mr4Reagents</option>
247 <option value="ProteinDatabase" >ProteinDatabase</option>
248 <option value="GeneLinkouts" >GeneLinkouts</option>
249 <option value="3dPreds" >3dPreds</option>
250 <option value="PdbSimilarities" >PdbSimilarities</option>
251 <option value="Epitopes" >Epitopes</option>
252 <option value="IsolateOverlap" >IsolateOverlap</option>
253 </param>
254 </when>
255 <when value="cached">
256 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/>
257 </when></conditional>
258 </when>
259 </conditional>
260 </inputs>
261 <outputs>
262 <data format="tabular" name="output" />
263 </outputs>
264 <help>
265 Replace white space with ** in all parameter values
266
267 .. class:: infomark
268
269 **TIP:** Organism type is xsd:string
270
271 .. class:: infomark
272
273 **TIP:** Include Pseudogenes type is xsd:string
274
275 .. class:: infomark
276
277 **TIP:** Gene type type is xsd:string
278 </help>
279 </tool>