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1 <tool id="client_38" name="genesbygenetype ">
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2 <description> Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl </description>
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3 <command interpreter="python">
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4 client_1.py
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5 #if $cond_source.optional_param_source=="no":
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6 $output
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7 $servicetype
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8 $url
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9 $method
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10 http://eupathdb.org/webservices/GeneQuestions
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11 organism
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12 #if $source0.source0_source=="user":
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13 $source0.user_param0
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14 #else:
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15 fileInput
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16 $source0.cached_param0
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17 #end if
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18 includePseudogenes
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19 #if $source1.source1_source=="user":
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20 $source1.user_param1
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21 #else:
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22 fileInput
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23 $source1.cached_param1
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24 #end if
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25 geneType
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26 #if $source2.source2_source=="user":
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27 $source2.user_param2
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28 #else:
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29 fileInput
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30 $source2.cached_param2
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31 #end if
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32 #else:
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33 $output
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34 $servicetype
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35 $url
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36 $method
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37 http://eupathdb.org/webservices/GeneQuestions
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38 organism
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39 #if $source0.source0_source=="user":
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40 $source0.user_param0
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41 #else:
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42 fileInput
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43 $source0.cached_param0
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44 #end if
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45 includePseudogenes
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46 #if $source1.source1_source=="user":
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47 $source1.user_param1
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48 #else:
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49 fileInput
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50 $source1.cached_param1
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51 #end if
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52 geneType
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53 #if $source2.source2_source=="user":
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54 $source2.user_param2
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55 #else:
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56 fileInput
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57 $source2.cached_param2
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58 #end if
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59 o-fields
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60 #if $cond_source.source3.source3_source=="user":
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61 $cond_source.source3.user_param3
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62 #else:
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63 fileInput
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64 $cond_source.source3.cached_param3
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65 #end if
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66 o-tables
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67 #if $cond_source.source4.source4_source=="user":
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68 $cond_source.source4.user_param4
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69 #else:
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70 fileInput
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71 $cond_source.source4.cached_param4
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72 #end if
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73 #end if
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74 </command>
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75 <inputs>
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76 <param name="servicetype" type="hidden" value="REST"/>
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77 <param name="url" type="hidden" value="http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl" />
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78 <param name="method" type="hidden" value="http://eupathdb.org/webservices/GeneQuestions" />
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79 <conditional name="source0">
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80 <param name="source0_source" type="select" label="Organism Source">
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81 <option value="cached" selected="true">Param value will be taken from previous step</option>
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82 <option value="user">User will enter the param value</option>
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83 </param>
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84 <when value="user">
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85 <param name="user_param0" type="select" label="Select Organism" help="see tip below">
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86 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
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87 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
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88 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
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89 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
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90 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
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91 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
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92 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
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93 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
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94 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
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95 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
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96 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
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97 <option value="Enterocytozoon**bieneusi" >Enterocytozoon bieneusi</option>
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98 <option value="Babesia**bovis" >Babesia bovis</option>
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99 <option value="Theileria**annulata" >Theileria annulata</option>
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100 <option value="Theileria**parva" >Theileria parva</option>
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101 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
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102 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
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103 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
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104 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
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105 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
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106 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
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107 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
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108 <option value="Neospora**caninum" >Neospora caninum</option>
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109 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
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110 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
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111 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
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112 <option value="Leishmania**infantum" >Leishmania infantum</option>
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113 <option value="Leishmania**major" >Leishmania major</option>
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114 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
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115 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
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116 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
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117 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
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118 </param>
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119 </when>
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120 <when value="cached">
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121 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/>
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122 </when></conditional><conditional name="source1">
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123 <param name="source1_source" type="select" label="Include Pseudogenes Source">
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124 <option value="cached" selected="true">Param value will be taken from previous step</option>
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125 <option value="user">User will enter the param value</option>
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126 </param>
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127 <when value="user">
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128 <param name="user_param1" type="select" label="Select Include Pseudogenes" help="see tip below">
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129 <option value="No" selected="true">No</option>
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130 <option value="Yes" >Yes</option>
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131 <option value="Pseudogenes**Only" >Pseudogenes Only</option>
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132 </param>
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133 </when>
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134 <when value="cached">
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135 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Include Pseudogenes"/>
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136 </when></conditional><conditional name="source2">
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137 <param name="source2_source" type="select" label="Gene type Source">
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138 <option value="cached" selected="true">Param value will be taken from previous step</option>
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139 <option value="user">User will enter the param value</option>
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140 </param>
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141 <when value="user">
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142 <param name="user_param2" type="select" label="Select Gene type" help="see tip below">
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143 <option value="protein**coding" selected="true">protein coding</option>
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144 <option value="snRNA**encoding" >snRNA encoding</option>
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145 <option value="tRNA**encoding" >tRNA encoding</option>
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146 <option value="rRNA**encoding" >rRNA encoding</option>
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147 <option value="misc**RNA" >misc RNA</option>
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148 <option value="snoRNA**encoding" >snoRNA encoding</option>
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149 <option value="SRP**RNA**encoding" >SRP RNA encoding</option>
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150 <option value="RNase**P**RNA" >RNase P RNA</option>
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151 <option value="RNase**MRP**RNA" >RNase MRP RNA</option>
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152 <option value="repeat**region" >repeat region</option>
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153 <option value="scRNA**encoding" >scRNA encoding</option>
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154 </param>
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155 </when>
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156 <when value="cached">
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157 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Gene type"/>
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158 </when></conditional> <conditional name="cond_source">
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159 <param name="optional_param_source" type="select" label="Display Additional Parameters">
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160 <option value="no" selected="true">no</option>
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161 <option value="yes">yes</option>
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162 </param>
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163 <when value="no">
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164 </when>
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165 <when value="yes">
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166
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167 <conditional name="source3">
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168 <param name="source3_source" type="select" label="Output Fields Source">
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169 <option value="cached" selected="true">Param value will be taken from previous step</option>
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170 <option value="user">User will enter the param value</option>
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171 </param>
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172 <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
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173 <option value="all" >all</option>
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174 <option value="none" selected="true">none</option>
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175 <option value="primary_key" >primary_key</option>
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176 <option value="formatted_gene_id" >formatted_gene_id</option>
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177 <option value="sequence_id" >sequence_id</option>
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178 <option value="chromosome" >chromosome</option>
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179 <option value="chromosome_order_num" >chromosome_order_num</option>
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180 <option value="location_text" >location_text</option>
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181 <option value="strand" >strand</option>
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182 <option value="gene_type" >gene_type</option>
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183 <option value="exon_count" >exon_count</option>
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184 <option value="transcript_length" >transcript_length</option>
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185 <option value="cds_length" >cds_length</option>
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186 <option value="product" >product</option>
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187 <option value="protein_length" >protein_length</option>
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188 <option value="tm_count" >tm_count</option>
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189 <option value="molecular_weight" >molecular_weight</option>
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190 <option value="isoelectric_point" >isoelectric_point</option>
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191 <option value="ec_numbers_string" >ec_numbers_string</option>
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192 <option value="ortholog_number" >ortholog_number</option>
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193 <option value="paralog_number" >paralog_number</option>
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194 <option value="orthomcl_name" >orthomcl_name</option>
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195 <option value="signalp_scores" >signalp_scores</option>
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196 <option value="signalp_peptide" >signalp_peptide</option>
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197 <option value="ann_go_function" >ann_go_function</option>
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198 <option value="ann_go_process" >ann_go_process</option>
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199 <option value="ann_go_component" >ann_go_component</option>
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200 <option value="pred_go_function" >pred_go_function</option>
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201 <option value="pred_go_process" >pred_go_process</option>
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202 <option value="pred_go_component" >pred_go_component</option>
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203 <option value="organism" >organism</option>
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204 <option value="is_pseudo" >is_pseudo</option>
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205 <option value="protein_sequence" >protein_sequence</option>
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206 <option value="transcript_sequence" >transcript_sequence</option>
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207 <option value="cds" >cds</option>
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208 <option value="wdk_weight" >wdk_weight</option>
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209 </param>
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210 </when>
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211 <when value="cached">
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212 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/>
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213 </when></conditional>
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214
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215 <conditional name="source4">
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216 <param name="source4_source" type="select" label="Output Tables Source">
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217 <option value="cached" selected="true">Param value will be taken from previous step</option>
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218 <option value="user">User will enter the param value</option>
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219 </param>
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220 <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
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221 <option value="all" >all</option>
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222 <option value="none" selected="true">none</option>
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223 <option value="SNPs" >SNPs</option>
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224 <option value="GeneModelDump" >GeneModelDump</option>
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225 <option value="InterPro" >InterPro</option>
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226 <option value="TMHMM" >TMHMM</option>
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227 <option value="LowComplexity" >LowComplexity</option>
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228 <option value="SignalP" >SignalP</option>
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229 <option value="BlastP" >BlastP</option>
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230 <option value="Genbank" >Genbank</option>
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231 <option value="SageTags" >SageTags</option>
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232 <option value="Notes" >Notes</option>
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233 <option value="UserComments" >UserComments</option>
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234 <option value="CommunityExpComments" >CommunityExpComments</option>
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235 <option value="EcNumber" >EcNumber</option>
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236 <option value="MassSpec" >MassSpec</option>
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237 <option value="GoTerms" >GoTerms</option>
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238 <option value="Phenotype" >Phenotype</option>
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239 <option value="Y2hInteractions" >Y2hInteractions</option>
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240 <option value="Orthologs" >Orthologs</option>
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241 <option value="MetabolicPathways" >MetabolicPathways</option>
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242 <option value="TaskComments" >TaskComments</option>
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243 <option value="ArrayElements" >ArrayElements</option>
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244 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
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245 <option value="ProteinExpression" >ProteinExpression</option>
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246 <option value="Mr4Reagents" >Mr4Reagents</option>
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247 <option value="ProteinDatabase" >ProteinDatabase</option>
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248 <option value="GeneLinkouts" >GeneLinkouts</option>
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249 <option value="3dPreds" >3dPreds</option>
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250 <option value="PdbSimilarities" >PdbSimilarities</option>
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251 <option value="Epitopes" >Epitopes</option>
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252 <option value="IsolateOverlap" >IsolateOverlap</option>
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253 </param>
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254 </when>
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255 <when value="cached">
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256 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/>
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257 </when></conditional>
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258 </when>
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259 </conditional>
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260 </inputs>
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261 <outputs>
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262 <data format="tabular" name="output" />
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263 </outputs>
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264 <help>
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265 Replace white space with ** in all parameter values
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266
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267 .. class:: infomark
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268
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269 **TIP:** Organism type is xsd:string
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270
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271 .. class:: infomark
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272
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273 **TIP:** Include Pseudogenes type is xsd:string
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274
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275 .. class:: infomark
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276
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277 **TIP:** Gene type type is xsd:string
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278 </help>
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279 </tool> |
