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comparison WebServiceToolWorkflow/workflowclients/client_4.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_4" 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 fileInput
13 $source0.cached_param0
14 #end if
15 min_molecular_weight
16 #if $source1.source1_source=="user":
17 $source1.user_param1
18 #else:
19 fileInput
20 $source1.cached_param1
21 #end if
22 max_molecular_weight
23 #if $source2.source2_source=="user":
24 $source2.user_param2
25 #else:
26 fileInput
27 $source2.cached_param2
28 #end if
29 #else:
30 $output
31 http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
32 organism
33 #if $source0.source0_source=="user":
34 $source0.user_param0
35 #else:
36 fileInput
37 $source0.cached_param0
38 #end if
39 min_molecular_weight
40 #if $source1.source1_source=="user":
41 $source1.user_param1
42 #else:
43 fileInput
44 $source1.cached_param1
45 #end if
46 max_molecular_weight
47 #if $source2.source2_source=="user":
48 $source2.user_param2
49 #else:
50 fileInput
51 $source2.cached_param2
52 #end if
53 o-fields
54 #if $source3.source3_source=="user":
55 $source3.user_param3
56 #else:
57 fileInput
58 $source3.cached_param3
59 #end if
60 o-tables
61 #if $source4.source4_source=="user":
62 $source4.user_param4
63 #else:
64 fileInput
65 $source4.cached_param4
66 #end if
67 #end if
68 </command>
69 <inputs>
70 <conditional name="source0">
71 <param name="source0_source" type="select" label="Organism Source">
72 <option value="cached" selected="true">Param value will be taken from previous step</option>
73 <option value="user">User will enter the param value</option>
74 </param>
75 <when value="user">
76 <param name="user_param0" type="select" label="Select Organism" help="see tip below">
77 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
78 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
79 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
80 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
81 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
82 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
83 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
84 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
85 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
86 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
87 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
88 <option value="Enterocytozoon**bieneusi" >Enterocytozoon bieneusi</option>
89 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
90 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
91 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
92 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
93 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
94 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
95 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
96 <option value="Neospora**caninum" >Neospora caninum</option>
97 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
98 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
99 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
100 <option value="Leishmania**infantum" >Leishmania infantum</option>
101 <option value="Leishmania**major" >Leishmania major</option>
102 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
103 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
104 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
105 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
106 </param>
107 </when>
108 <when value="cached">
109 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/>
110 </when></conditional><conditional name="source1">
111 <param name="source1_source" type="select" label="Min Molecular Weight (Daltons) Source">
112 <option value="cached" selected="true">Param value will be taken from previous step</option>
113 <option value="user">User will enter the param value</option>
114 </param>
115 <when value="user">
116 <param format="text" size = "150" name = "user_param1" value="10000" type="text" label="Enter Min Molecular Weight (Daltons)" help="see tip below" />
117 </when>
118 <when value="cached">
119 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Min Molecular Weight (Daltons)"/>
120 </when></conditional><conditional name="source2">
121 <param name="source2_source" type="select" label="Max Molecular Weight (Daltons) Source">
122 <option value="cached" selected="true">Param value will be taken from previous step</option>
123 <option value="user">User will enter the param value</option>
124 </param>
125 <when value="user">
126 <param format="text" size = "150" name = "user_param2" value="50000" type="text" label="Enter Max Molecular Weight (Daltons)" help="see tip below" />
127 </when>
128 <when value="cached">
129 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Max Molecular Weight (Daltons)"/>
130 </when></conditional> <conditional name="cond_source">
131 <param name="optional_param_source" type="select" label="Display Additional Parameters">
132 <option value="no" selected="true">no</option>
133 <option value="yes">yes</option>
134 </param>
135 <when value="no">
136 </when>
137 <when value="yes">
138
139 <conditional name="source3">
140 <param name="source3_source" type="select" label="Output Fields Source">
141 <option value="cached" selected="true">Param value will be taken from previous step</option>
142 <option value="user">User will enter the param value</option>
143 </param>
144 <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
145 <option value="all" >all</option>
146 <option value="none" selected="true">none</option>
147 <option value="primary_key" >primary_key</option>
148 <option value="formatted_gene_id" >formatted_gene_id</option>
149 <option value="external_db_name" >external_db_name</option>
150 <option value="sequence_id" >sequence_id</option>
151 <option value="chromosome" >chromosome</option>
152 <option value="location_text" >location_text</option>
153 <option value="strand" >strand</option>
154 <option value="gene_type" >gene_type</option>
155 <option value="exon_count" >exon_count</option>
156 <option value="transcript_length" >transcript_length</option>
157 <option value="cds_length" >cds_length</option>
158 <option value="product" >product</option>
159 <option value="protein_length" >protein_length</option>
160 <option value="tm_count" >tm_count</option>
161 <option value="molecular_weight" >molecular_weight</option>
162 <option value="isoelectric_point" >isoelectric_point</option>
163 <option value="ec_numbers_string" >ec_numbers_string</option>
164 <option value="ortholog_number" >ortholog_number</option>
165 <option value="paralog_number" >paralog_number</option>
166 <option value="orthomcl_name" >orthomcl_name</option>
167 <option value="signalp_scores" >signalp_scores</option>
168 <option value="signalp_peptide" >signalp_peptide</option>
169 <option value="ann_go_function" >ann_go_function</option>
170 <option value="ann_go_process" >ann_go_process</option>
171 <option value="ann_go_component" >ann_go_component</option>
172 <option value="pred_go_function" >pred_go_function</option>
173 <option value="pred_go_process" >pred_go_process</option>
174 <option value="pred_go_component" >pred_go_component</option>
175 <option value="organism" >organism</option>
176 <option value="protein_sequence" >protein_sequence</option>
177 <option value="transcript_sequence" >transcript_sequence</option>
178 <option value="cds" >cds</option>
179 <option value="wdk_weight" >wdk_weight</option>
180 </param>
181 </when>
182 <when value="cached">
183 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/>
184 </when></conditional>
185
186 <conditional name="source4">
187 <param name="source4_source" type="select" label="Output Tables Source">
188 <option value="cached" selected="true">Param value will be taken from previous step</option>
189 <option value="user">User will enter the param value</option>
190 </param>
191 <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
192 <option value="all" >all</option>
193 <option value="none" selected="true">none</option>
194 <option value="SNPs" >SNPs</option>
195 <option value="GeneModelDump" >GeneModelDump</option>
196 <option value="InterPro" >InterPro</option>
197 <option value="TMHMM" >TMHMM</option>
198 <option value="LowComplexity" >LowComplexity</option>
199 <option value="SignalP" >SignalP</option>
200 <option value="BlastP" >BlastP</option>
201 <option value="Genbank" >Genbank</option>
202 <option value="SageTags" >SageTags</option>
203 <option value="Notes" >Notes</option>
204 <option value="UserComments" >UserComments</option>
205 <option value="CommunityExpComments" >CommunityExpComments</option>
206 <option value="EcNumber" >EcNumber</option>
207 <option value="GoTerms" >GoTerms</option>
208 <option value="Aliases" >Aliases</option>
209 <option value="Phenotype" >Phenotype</option>
210 <option value="Y2hInteractions" >Y2hInteractions</option>
211 <option value="Orthologs" >Orthologs</option>
212 <option value="MetabolicPathways" >MetabolicPathways</option>
213 <option value="TaskComments" >TaskComments</option>
214 <option value="ArrayElements" >ArrayElements</option>
215 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
216 <option value="ProteinExpression" >ProteinExpression</option>
217 <option value="Mr4Reagents" >Mr4Reagents</option>
218 <option value="ProteinDatabase" >ProteinDatabase</option>
219 <option value="GeneLinkouts" >GeneLinkouts</option>
220 <option value="3dPreds" >3dPreds</option>
221 <option value="PdbSimilarities" >PdbSimilarities</option>
222 <option value="Epitopes" >Epitopes</option>
223 <option value="IsolateOverlap" >IsolateOverlap</option>
224 </param>
225 </when>
226 <when value="cached">
227 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/>
228 </when></conditional>
229 </when>
230 </conditional>
231 </inputs>
232 <outputs>
233 <data format="tabular" name="output" />
234 </outputs>
235 <help>
236 Replace white space with ** in all parameter values
237
238 .. class:: infomark
239
240 **TIP:** Organism type is xsd:string
241
242 .. class:: infomark
243
244 **TIP:** Min Molecular Weight (Daltons) type is xsd:string
245
246 .. class:: infomark
247
248 **TIP:** Max Molecular Weight (Daltons) type is xsd:string
249 </help>
250 </tool>