Mercurial > repos > uga-galaxy-group > webservice_toolsuite_v1_1
comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/clients/client_3.xml~ @ 0:049760c677de default tip
Galaxy WSExtensions added successfully
author | uga-galaxy-group |
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date | Tue, 05 Jul 2011 19:34:18 -0400 |
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1 <tool id="client_31" name="genesbygenetype "> | |
2 <description> Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl </description> | |
3 <command interpreter="python"> | |
4 #if $cond_source.optional_param_source=="no" #client_1.py $output $service http://eupathdb.org/webservices/GeneQuestions/GenesByGeneType.xml organism $param0 includePseudogenes $param1 geneType $param2 #else #client_1.py $output $service http://eupathdb.org/webservices/GeneQuestions/GenesByGeneType.xml organism $param0 includePseudogenes $param1 geneType $param2 o-fields $cond_source.param3 o-tables $cond_source.param4 #end if | |
5 </command> | |
6 <inputs> | |
7 <param name='service' type='hidden' value='REST'/> | |
8 <param name="param0" type="select" label="Select Organism" help="see tip below"> | |
9 <option value="Entamoeba**dispar" >Entamoeba dispar</option> | |
10 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option> | |
11 <option value="Entamoeba**invadens" >Entamoeba invadens</option> | |
12 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option> | |
13 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option> | |
14 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option> | |
15 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option> | |
16 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option> | |
17 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option> | |
18 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option> | |
19 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option> | |
20 <option value="Enterocytozoon**bieneusi" >Enterocytozoon bieneusi</option> | |
21 <option value="Babesia**bovis" >Babesia bovis</option> | |
22 <option value="Theileria**annulata" >Theileria annulata</option> | |
23 <option value="Theileria**parva" >Theileria parva</option> | |
24 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option> | |
25 <option value="Plasmodium**vivax" >Plasmodium vivax</option> | |
26 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option> | |
27 <option value="Plasmodium**berghei" >Plasmodium berghei</option> | |
28 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option> | |
29 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option> | |
30 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option> | |
31 <option value="Neospora**caninum" >Neospora caninum</option> | |
32 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option> | |
33 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option> | |
34 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option> | |
35 <option value="Leishmania**infantum" >Leishmania infantum</option> | |
36 <option value="Leishmania**major" >Leishmania major</option> | |
37 <option value="Leishmania**mexicana" >Leishmania mexicana</option> | |
38 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option> | |
39 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option> | |
40 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option> | |
41 </param> | |
42 <param name="param1" type="select" label="Select Include Pseudogenes" help="see tip below"> | |
43 <option value="No" selected="true">No</option> | |
44 <option value="Yes" >Yes</option> | |
45 <option value="Pseudogenes**Only" >Pseudogenes Only</option> | |
46 </param> | |
47 <param name="param2" type="select" label="Select Gene type" help="see tip below"> | |
48 <option value="protein**coding" selected="true">protein coding</option> | |
49 <option value="snRNA**encoding" >snRNA encoding</option> | |
50 <option value="tRNA**encoding" >tRNA encoding</option> | |
51 <option value="rRNA**encoding" >rRNA encoding</option> | |
52 <option value="misc**RNA" >misc RNA</option> | |
53 <option value="snoRNA**encoding" >snoRNA encoding</option> | |
54 <option value="SRP**RNA**encoding" >SRP RNA encoding</option> | |
55 <option value="RNase**P**RNA" >RNase P RNA</option> | |
56 <option value="RNase**MRP**RNA" >RNase MRP RNA</option> | |
57 <option value="repeat**region" >repeat region</option> | |
58 <option value="scRNA**encoding" >scRNA encoding</option> | |
59 </param> | |
60 | |
61 <conditional name="cond_source"> | |
62 <param name="optional_param_source" type="select" label="Show Additional Parameters"> | |
63 <option value="no" selected="true">no</option> | |
64 <option value="yes">yes</option> | |
65 </param> | |
66 <when value="no"> | |
67 </when><when value="yes"> | |
68 <param name="param3" type="select" label="Select Output Fields" help="see tip below"> | |
69 <option value="all" >all</option> | |
70 <option value="none" selected="true">none</option> | |
71 <option value="primary_key" >primary_key</option> | |
72 <option value="formatted_gene_id" >formatted_gene_id</option> | |
73 <option value="sequence_id" >sequence_id</option> | |
74 <option value="chromosome" >chromosome</option> | |
75 <option value="chromosome_order_num" >chromosome_order_num</option> | |
76 <option value="location_text" >location_text</option> | |
77 <option value="strand" >strand</option> | |
78 <option value="gene_type" >gene_type</option> | |
79 <option value="exon_count" >exon_count</option> | |
80 <option value="transcript_length" >transcript_length</option> | |
81 <option value="cds_length" >cds_length</option> | |
82 <option value="product" >product</option> | |
83 <option value="protein_length" >protein_length</option> | |
84 <option value="tm_count" >tm_count</option> | |
85 <option value="molecular_weight" >molecular_weight</option> | |
86 <option value="isoelectric_point" >isoelectric_point</option> | |
87 <option value="ec_numbers_string" >ec_numbers_string</option> | |
88 <option value="ortholog_number" >ortholog_number</option> | |
89 <option value="paralog_number" >paralog_number</option> | |
90 <option value="orthomcl_name" >orthomcl_name</option> | |
91 <option value="signalp_scores" >signalp_scores</option> | |
92 <option value="signalp_peptide" >signalp_peptide</option> | |
93 <option value="ann_go_function" >ann_go_function</option> | |
94 <option value="ann_go_process" >ann_go_process</option> | |
95 <option value="ann_go_component" >ann_go_component</option> | |
96 <option value="pred_go_function" >pred_go_function</option> | |
97 <option value="pred_go_process" >pred_go_process</option> | |
98 <option value="pred_go_component" >pred_go_component</option> | |
99 <option value="organism" >organism</option> | |
100 <option value="is_pseudo" >is_pseudo</option> | |
101 <option value="protein_sequence" >protein_sequence</option> | |
102 <option value="transcript_sequence" >transcript_sequence</option> | |
103 <option value="cds" >cds</option> | |
104 <option value="wdk_weight" >wdk_weight</option> | |
105 </param> | |
106 <param name="param4" type="select" label="Select Output Tables" help="see tip below"> | |
107 <option value="all" >all</option> | |
108 <option value="none" selected="true">none</option> | |
109 <option value="SNPs" >SNPs</option> | |
110 <option value="GeneModelDump" >GeneModelDump</option> | |
111 <option value="InterPro" >InterPro</option> | |
112 <option value="TMHMM" >TMHMM</option> | |
113 <option value="LowComplexity" >LowComplexity</option> | |
114 <option value="SignalP" >SignalP</option> | |
115 <option value="BlastP" >BlastP</option> | |
116 <option value="Genbank" >Genbank</option> | |
117 <option value="SageTags" >SageTags</option> | |
118 <option value="Notes" >Notes</option> | |
119 <option value="UserComments" >UserComments</option> | |
120 <option value="CommunityExpComments" >CommunityExpComments</option> | |
121 <option value="EcNumber" >EcNumber</option> | |
122 <option value="MassSpec" >MassSpec</option> | |
123 <option value="GoTerms" >GoTerms</option> | |
124 <option value="Phenotype" >Phenotype</option> | |
125 <option value="Y2hInteractions" >Y2hInteractions</option> | |
126 <option value="Orthologs" >Orthologs</option> | |
127 <option value="MetabolicPathways" >MetabolicPathways</option> | |
128 <option value="TaskComments" >TaskComments</option> | |
129 <option value="ArrayElements" >ArrayElements</option> | |
130 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option> | |
131 <option value="ProteinExpression" >ProteinExpression</option> | |
132 <option value="Mr4Reagents" >Mr4Reagents</option> | |
133 <option value="ProteinDatabase" >ProteinDatabase</option> | |
134 <option value="GeneLinkouts" >GeneLinkouts</option> | |
135 <option value="3dPreds" >3dPreds</option> | |
136 <option value="PdbSimilarities" >PdbSimilarities</option> | |
137 <option value="Epitopes" >Epitopes</option> | |
138 <option value="IsolateOverlap" >IsolateOverlap</option> | |
139 </param> | |
140 </when> | |
141 </conditional></inputs> | |
142 <outputs> | |
143 <data format="tabular" name="output" /> | |
144 </outputs> | |
145 <help> | |
146 Replace white space with ** in all parameter values | |
147 | |
148 .. class:: infomark | |
149 | |
150 **TIP:** Organism type is xsd:string | |
151 | |
152 .. class:: infomark | |
153 | |
154 **TIP:** Include Pseudogenes type is xsd:string | |
155 | |
156 .. class:: infomark | |
157 | |
158 **TIP:** Gene type type is xsd:string | |
159 </help> | |
160 </tool> |