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1 <tool id="client_1" name="genesbytextsearch">
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2 <description> Client for method: genesbytextsearch , Web service: /home/ganjoo/parser/SAWADLParser/euPathWADL/GenesByTextSearch.sawadl </description>
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3 <command interpreter="python">
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4 client_1.py
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5 $output
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6 http://eupathdb.org/webservices/GeneQuestions/GenesByTextSearch.xml
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7 text_search_organism
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8 $source0.user_param0
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9 text_expression
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10 $param1
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11 text_fields
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12 $param2
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13 whole_words
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14 $param3
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15 max_pvalue
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16 $param4
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17 </command>
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18 <inputs>
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19 <conditional name="source0">
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20 <param name="source0_source" type="select" label="text_search_organism Source">
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21 <option value="cached" selected="true">Param value will be taken from previous step</option>
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22 <option value="user">User will enter the param value</option>
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23 </param>
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24 <when value="user">
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25 <param name="user_param0" type="select" label="text_search_organism" help="see tip below">
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26 <option value="Entamoeba**dispar" selected="true">Entamoeba dispar</option>
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27 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
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28 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
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29 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
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30 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
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31 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
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32 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
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33 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
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34 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
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35 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
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36 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
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37 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
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38 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
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39 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
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40 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
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41 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
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42 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
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43 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
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44 <option value="Neospora**caninum" >Neospora caninum</option>
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45 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
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46 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
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47 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
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48 <option value="Leishmania**infantum" >Leishmania infantum</option>
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49 <option value="Leishmania**major" >Leishmania major</option>
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50 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
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51 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
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52 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
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53 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
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54 </param>
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55 </when>
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56 <when value="cached">
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57 <param name = "cached_param0" type="data" label="Choose the step from which to get the SAWADL location"/>
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58 </when>
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59 </conditional>
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60 <param format="text" size = "150" name = "param1" value="membrane" type="text" label="text_expression" help="see tip below" />
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61 <param name="param2" type="select" label="text_fields" help="see tip below">
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62 <option value="Gene**ID" >Gene ID</option>
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63 <option value="Alias" >Alias</option>
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64 <option value="Gene**product" selected="true">Gene product</option>
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65 <option value="Phenotype" >Phenotype</option>
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66 <option value="GO**terms**and**definitions" >GO terms and definitions</option>
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67 <option value="Gene**notes" >Gene notes</option>
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68 <option value="User**comments" >User comments</option>
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69 <option value="Protein**domain**names**and**descriptions" >Protein domain names and descriptions</option>
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70 <option value="Similar**proteins**(BLAST**hits**v.**NRDB/PDB)" >Similar proteins (BLAST hits v. NRDB/PDB)</option>
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71 <option value="EC**descriptions" >EC descriptions</option>
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72 <option value="Metabolic**pathway**names**and**descriptions" >Metabolic pathway names and descriptions</option>
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73 </param>
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74 <param name="param3" type="select" label="whole_words" help="see tip below">
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75 <option value="yes" >yes</option>
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76 <option value="no" selected="true">no</option>
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77 </param>
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78 <param format="text" size = "150" name = "param4" value="-30" type="text" label="max_pvalue" help="see tip below" />
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79 </inputs>
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80 <outputs>
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81 <data format="tabular" name="output" />
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82 </outputs>
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83 <help>
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84
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85 .. class:: infomark
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86
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87 **TIP:** About text_search_organism: type is xsd:string, description from ontology is "Organism identifier"
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88
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89 .. class:: infomark
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90
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91 **TIP:** About text_expression: type is xsd:string, description from ontology is "This term can be used for any free-form comments and annotations."
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92
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93 .. class:: infomark
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94
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95 **TIP:** About text_fields: type is xsd:string, description from ontology is "Undefined concept"
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96
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97 .. class:: infomark
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98
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99 **TIP:** About whole_words: type is xsd:string, description from ontology is "
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100 A simple parameter that is a toggle (boolean value), typically a control for a modal tool
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101 "
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102
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103 .. class:: infomark
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104
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105 **TIP:** About max_pvalue: type is xsd:string
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106 </help>
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107 </tool>
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