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comparison WebServiceToolWorkflow/clients/client_5.xml~ @ 0:d5cd409b8a18 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author ganjoo
date Tue, 07 Jun 2011 18:00:50 -0400
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-1:000000000000 0:d5cd409b8a18
1 <tool id="client_51" name="genesbymolecularweight">
2 <description> Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl </description>
3 <command interpreter="python">
4 #if $cond_source.optional_param_source=="no" #client_1.py $output http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml organism $param0 min_molecular_weight $param1 max_molecular_weight $param2#else #client_1.py $output http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml organism $param0 min_molecular_weight $param1 max_molecular_weight $param2 o-fields $cond_source.param3 o-tables $cond_source.param4#end if
5 </command>
6 <inputs>
7 <param name="param0" type="select" label="organism" help="see tip below">
8 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
9 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
10 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
11 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
12 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
13 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
14 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
15 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
16 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
17 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
18 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
19 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
20 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
21 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
22 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
23 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
24 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
25 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
26 <option value="Neospora**caninum" >Neospora caninum</option>
27 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
28 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
29 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
30 <option value="Leishmania**infantum" >Leishmania infantum</option>
31 <option value="Leishmania**major" >Leishmania major</option>
32 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
33 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
34 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
35 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
36 </param>
37 <param format="text" size = "150" name = "param1" type="text" label="min_molecular_weight" help="see tip below" />
38 <param format="text" size = "150" name = "param2" type="text" label="max_molecular_weight" help="see tip below" />
39
40 <conditional name="cond_source">
41 <param name="optional_param_source" type="select" label="Help">
42 <option value="no" selected="true">no</option>
43 <option value="yes">yes</option>
44 </param>
45 <when value="no">
46 </when><when value="yes">
47 <param name="param3" type="select" label="o-fields" help="see tip below">
48 <option value="all" >all</option>
49 <option value="none" selected="true">none</option>
50 <option value="primary_key" >primary_key</option>
51 <option value="formatted_gene_id" >formatted_gene_id</option>
52 <option value="external_db_name" >external_db_name</option>
53 <option value="sequence_id" >sequence_id</option>
54 <option value="chromosome" >chromosome</option>
55 <option value="location_text" >location_text</option>
56 <option value="strand" >strand</option>
57 <option value="gene_type" >gene_type</option>
58 <option value="exon_count" >exon_count</option>
59 <option value="transcript_length" >transcript_length</option>
60 <option value="cds_length" >cds_length</option>
61 <option value="product" >product</option>
62 <option value="protein_length" >protein_length</option>
63 <option value="tm_count" >tm_count</option>
64 <option value="molecular_weight" >molecular_weight</option>
65 <option value="isoelectric_point" >isoelectric_point</option>
66 <option value="ec_numbers_string" >ec_numbers_string</option>
67 <option value="ortholog_number" >ortholog_number</option>
68 <option value="paralog_number" >paralog_number</option>
69 <option value="orthomcl_name" >orthomcl_name</option>
70 <option value="signalp_scores" >signalp_scores</option>
71 <option value="signalp_peptide" >signalp_peptide</option>
72 <option value="ann_go_function" >ann_go_function</option>
73 <option value="ann_go_process" >ann_go_process</option>
74 <option value="ann_go_component" >ann_go_component</option>
75 <option value="pred_go_function" >pred_go_function</option>
76 <option value="pred_go_process" >pred_go_process</option>
77 <option value="pred_go_component" >pred_go_component</option>
78 <option value="organism" >organism</option>
79 <option value="protein_sequence" >protein_sequence</option>
80 <option value="transcript_sequence" >transcript_sequence</option>
81 <option value="cds" >cds</option>
82 <option value="wdk_weight" >wdk_weight</option>
83 </param>
84 <param name="param4" type="select" label="o-tables" help="see tip below">
85 <option value="all" >all</option>
86 <option value="none" selected="true">none</option>
87 <option value="SNPs" >SNPs</option>
88 <option value="GeneModelDump" >GeneModelDump</option>
89 <option value="InterPro" >InterPro</option>
90 <option value="TMHMM" >TMHMM</option>
91 <option value="LowComplexity" >LowComplexity</option>
92 <option value="SignalP" >SignalP</option>
93 <option value="BlastP" >BlastP</option>
94 <option value="Genbank" >Genbank</option>
95 <option value="SageTags" >SageTags</option>
96 <option value="Notes" >Notes</option>
97 <option value="UserComments" >UserComments</option>
98 <option value="CommunityExpComments" >CommunityExpComments</option>
99 <option value="EcNumber" >EcNumber</option>
100 <option value="MassSpec" >MassSpec</option>
101 <option value="GoTerms" >GoTerms</option>
102 <option value="Aliases" >Aliases</option>
103 <option value="Phenotype" >Phenotype</option>
104 <option value="Y2hInteractions" >Y2hInteractions</option>
105 <option value="Orthologs" >Orthologs</option>
106 <option value="MetabolicPathways" >MetabolicPathways</option>
107 <option value="TaskComments" >TaskComments</option>
108 <option value="ArrayElements" >ArrayElements</option>
109 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
110 <option value="ProteinExpression" >ProteinExpression</option>
111 <option value="Mr4Reagents" >Mr4Reagents</option>
112 <option value="ProteinDatabase" >ProteinDatabase</option>
113 <option value="GeneLinkouts" >GeneLinkouts</option>
114 <option value="3dPreds" >3dPreds</option>
115 <option value="PdbSimilarities" >PdbSimilarities</option>
116 <option value="Epitopes" >Epitopes</option>
117 <option value="IsolateOverlap" >IsolateOverlap</option>
118 </param>
119 </when>
120 </conditional></inputs>
121 <outputs>
122 <data format="tabular" name="output" />
123 </outputs>
124 <help>
125
126 .. class:: infomark
127
128 **TIP:** organism type is xsd:string
129
130 .. class:: infomark
131
132 **TIP:** min_molecular_weight type is xsd:string
133
134 .. class:: infomark
135
136 **TIP:** max_molecular_weight type is xsd:string
137 </help>
138 </tool>