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comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.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_2" name="genesbymolecularweight ">
2 <description> Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl </description>
3 <command interpreter="python">
4 client_1.py
5 #if $cond_source.optional_param_source=="no":
6 $output
7 http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
8 organism
9 #if $source0.source0_source=="user":
10 $source0.user_param0
11 #else:
12 $source0.cached_param0
13 #end if
14 min_molecular_weight
15 #if $source1.source1_source=="user":
16 $source1.user_param1
17 #else:
18 $source1.cached_param1
19 #end if
20 max_molecular_weight
21 #if $source2.source2_source=="user":
22 $source2.user_param2
23 #else:
24 $source2.cached_param2
25 #end if
26 #else:
27 organism
28 #if $source0.source0_source=="user":
29 $source0.user_param0
30 #else:
31 $source0.cached_param0
32 #end if
33 min_molecular_weight
34 #if $source1.source1_source=="user":
35 $source1.user_param1
36 #else:
37 $source1.cached_param1
38 #end if
39 max_molecular_weight
40 #if $source2.source2_source=="user":
41 $source2.user_param2
42 #else:
43 $source2.cached_param2
44 #end if
45 o-fields
46 #if $cond_source.source3.source3_source=="user":
47 $cond_source.source3.user_param3
48 #else:
49 $cond_source.source3.cached_param3
50 #end if
51 o-tables
52 #if $cond_source.source4.source4_source=="user":
53 $cond_source.source4.user_param4
54 #else:
55 $cond_source.source4.cached_param4
56 #end if
57 #end if
58 </command>
59 <inputs>
60 <conditional name="source0">
61 <param name="source0_source" type="select" label="Organism Source">
62 <option value="cached" selected="true">Param value will be taken from previous step</option>
63 <option value="user">User will enter the param value</option>
64 </param>
65 <when value="user">
66 <param name="user_param0" type="select" label="Select Organism" help="see tip below">
67 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
68 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
69 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
70 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
71 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
72 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
73 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
74 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
75 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
76 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
77 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
78 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
79 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
80 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
81 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
82 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
83 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
84 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
85 <option value="Neospora**caninum" >Neospora caninum</option>
86 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
87 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
88 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
89 <option value="Leishmania**infantum" >Leishmania infantum</option>
90 <option value="Leishmania**major" >Leishmania major</option>
91 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
92 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
93 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
94 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
95 </param>
96 </when>
97 <when value="cached">
98 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/>
99 </when></conditional><conditional name="source1">
100 <param name="source1_source" type="select" label="Min Molecular Weight (Daltons) Source">
101 <option value="cached" selected="true">Param value will be taken from previous step</option>
102 <option value="user">User will enter the param value</option>
103 </param>
104 <when value="user">
105 <param format="text" size = "150" name = "user_param1" type="text" label="Enter Min Molecular Weight (Daltons)" help="see tip below" />
106 </when>
107 <when value="cached">
108 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Min Molecular Weight (Daltons)"/>
109 </when></conditional><conditional name="source2">
110 <param name="source2_source" type="select" label="Max Molecular Weight (Daltons) Source">
111 <option value="cached" selected="true">Param value will be taken from previous step</option>
112 <option value="user">User will enter the param value</option>
113 </param>
114 <when value="user">
115 <param format="text" size = "150" name = "user_param2" type="text" label="Enter Max Molecular Weight (Daltons)" help="see tip below" />
116 </when>
117 <when value="cached">
118 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Max Molecular Weight (Daltons)"/>
119 </when></conditional> <conditional name="cond_source">
120 <param name="optional_param_source" type="select" label="Display Additional Parameters">
121 <option value="no" selected="true">no</option>
122 <option value="yes">yes</option>
123 </param>
124 <when value="no">
125 </when>
126 <when value="yes">
127
128 <conditional name="source3">
129 <param name="source3_source" type="select" label="Output Fields Source">
130 <option value="cached" selected="true">Param value will be taken from previous step</option>
131 <option value="user">User will enter the param value</option>
132 </param>
133 <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
134 <option value="all" >all</option>
135 <option value="none" selected="true">none</option>
136 <option value="primary_key" >primary_key</option>
137 <option value="formatted_gene_id" >formatted_gene_id</option>
138 <option value="external_db_name" >external_db_name</option>
139 <option value="sequence_id" >sequence_id</option>
140 <option value="chromosome" >chromosome</option>
141 <option value="location_text" >location_text</option>
142 <option value="strand" >strand</option>
143 <option value="gene_type" >gene_type</option>
144 <option value="exon_count" >exon_count</option>
145 <option value="transcript_length" >transcript_length</option>
146 <option value="cds_length" >cds_length</option>
147 <option value="product" >product</option>
148 <option value="protein_length" >protein_length</option>
149 <option value="tm_count" >tm_count</option>
150 <option value="molecular_weight" >molecular_weight</option>
151 <option value="isoelectric_point" >isoelectric_point</option>
152 <option value="ec_numbers_string" >ec_numbers_string</option>
153 <option value="ortholog_number" >ortholog_number</option>
154 <option value="paralog_number" >paralog_number</option>
155 <option value="orthomcl_name" >orthomcl_name</option>
156 <option value="signalp_scores" >signalp_scores</option>
157 <option value="signalp_peptide" >signalp_peptide</option>
158 <option value="ann_go_function" >ann_go_function</option>
159 <option value="ann_go_process" >ann_go_process</option>
160 <option value="ann_go_component" >ann_go_component</option>
161 <option value="pred_go_function" >pred_go_function</option>
162 <option value="pred_go_process" >pred_go_process</option>
163 <option value="pred_go_component" >pred_go_component</option>
164 <option value="organism" >organism</option>
165 <option value="protein_sequence" >protein_sequence</option>
166 <option value="transcript_sequence" >transcript_sequence</option>
167 <option value="cds" >cds</option>
168 <option value="wdk_weight" >wdk_weight</option>
169 </param>
170 </when>
171 <when value="cached">
172 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/>
173 </when></conditional>
174
175 <conditional name="source4">
176 <param name="source4_source" type="select" label="Output Tables Source">
177 <option value="cached" selected="true">Param value will be taken from previous step</option>
178 <option value="user">User will enter the param value</option>
179 </param>
180 <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
181 <option value="all" >all</option>
182 <option value="none" selected="true">none</option>
183 <option value="SNPs" >SNPs</option>
184 <option value="GeneModelDump" >GeneModelDump</option>
185 <option value="InterPro" >InterPro</option>
186 <option value="TMHMM" >TMHMM</option>
187 <option value="LowComplexity" >LowComplexity</option>
188 <option value="SignalP" >SignalP</option>
189 <option value="BlastP" >BlastP</option>
190 <option value="Genbank" >Genbank</option>
191 <option value="SageTags" >SageTags</option>
192 <option value="Notes" >Notes</option>
193 <option value="UserComments" >UserComments</option>
194 <option value="CommunityExpComments" >CommunityExpComments</option>
195 <option value="EcNumber" >EcNumber</option>
196 <option value="MassSpec" >MassSpec</option>
197 <option value="GoTerms" >GoTerms</option>
198 <option value="Aliases" >Aliases</option>
199 <option value="Phenotype" >Phenotype</option>
200 <option value="Y2hInteractions" >Y2hInteractions</option>
201 <option value="Orthologs" >Orthologs</option>
202 <option value="MetabolicPathways" >MetabolicPathways</option>
203 <option value="TaskComments" >TaskComments</option>
204 <option value="ArrayElements" >ArrayElements</option>
205 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
206 <option value="ProteinExpression" >ProteinExpression</option>
207 <option value="Mr4Reagents" >Mr4Reagents</option>
208 <option value="ProteinDatabase" >ProteinDatabase</option>
209 <option value="GeneLinkouts" >GeneLinkouts</option>
210 <option value="3dPreds" >3dPreds</option>
211 <option value="PdbSimilarities" >PdbSimilarities</option>
212 <option value="Epitopes" >Epitopes</option>
213 <option value="IsolateOverlap" >IsolateOverlap</option>
214 </param>
215 </when>
216 <when value="cached">
217 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/>
218 </when></conditional>
219 </when>
220 </conditional>
221 </inputs>
222 <outputs>
223 <data format="tabular" name="output" />
224 </outputs>
225 <help>
226
227 .. class:: infomark
228
229 **TIP:** Organism type is xsd:string
230
231 .. class:: infomark
232
233 **TIP:** Min Molecular Weight (Daltons) type is xsd:string
234
235 .. class:: infomark
236
237 **TIP:** Max Molecular Weight (Daltons) type is xsd:string
238 </help>
239 </tool>