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1 <tool id="client_2" name="genesbymolecularweight ">
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2 <description> Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.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 http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
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8 organism
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9 #if $source0.source0_source=="user":
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10 $source0.user_param0
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11 #else:
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12 $source0.cached_param0
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13 #end if
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14 min_molecular_weight
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15 #if $source1.source1_source=="user":
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16 $source1.user_param1
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17 #else:
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18 $source1.cached_param1
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19 #end if
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20 max_molecular_weight
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21 #if $source2.source2_source=="user":
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22 $source2.user_param2
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23 #else:
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24 $source2.cached_param2
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25 #end if
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26 #else:
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27 organism
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28 #if $source0.source0_source=="user":
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29 $source0.user_param0
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30 #else:
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31 $source0.cached_param0
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32 #end if
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33 min_molecular_weight
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34 #if $source1.source1_source=="user":
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35 $source1.user_param1
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36 #else:
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37 $source1.cached_param1
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38 #end if
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39 max_molecular_weight
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40 #if $source2.source2_source=="user":
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41 $source2.user_param2
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42 #else:
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43 $source2.cached_param2
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44 #end if
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45 o-fields
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46 #if $cond_source.source3.source3_source=="user":
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47 $cond_source.source3.user_param3
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48 #else:
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49 $cond_source.source3.cached_param3
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50 #end if
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51 o-tables
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52 #if $cond_source.source4.source4_source=="user":
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53 $cond_source.source4.user_param4
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54 #else:
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55 $cond_source.source4.cached_param4
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56 #end if
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57 #end if
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58 </command>
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59 <inputs>
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60 <conditional name="source0">
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61 <param name="source0_source" type="select" label="Organism Source">
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62 <option value="cached" selected="true">Param value will be taken from previous step</option>
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63 <option value="user">User will enter the param value</option>
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64 </param>
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65 <when value="user">
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66 <param name="user_param0" type="select" label="Select Organism" help="see tip below">
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67 <option value="Entamoeba**dispar" >Entamoeba dispar</option>
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68 <option value="Entamoeba**histolytica" >Entamoeba histolytica</option>
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69 <option value="Entamoeba**invadens" >Entamoeba invadens</option>
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70 <option value="Cryptosporidium**parvum" >Cryptosporidium parvum</option>
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71 <option value="Cryptosporidium**hominis" >Cryptosporidium hominis</option>
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72 <option value="Cryptosporidium**muris" >Cryptosporidium muris</option>
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73 <option value="Giardia**Assemblage**A**isolate**WB" >Giardia Assemblage A isolate WB</option>
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74 <option value="Giardia**Assemblage**B**isolate**GS" >Giardia Assemblage B isolate GS</option>
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75 <option value="Giardia**Assemblage**E**isolate**P15" >Giardia Assemblage E isolate P15</option>
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76 <option value="Encephalitozoon**cuniculi" >Encephalitozoon cuniculi</option>
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77 <option value="Encephalitozoon**intestinalis" >Encephalitozoon intestinalis</option>
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78 <option value="Plasmodium**falciparum" >Plasmodium falciparum</option>
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79 <option value="Plasmodium**vivax" >Plasmodium vivax</option>
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80 <option value="Plasmodium**yoelii" >Plasmodium yoelii</option>
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81 <option value="Plasmodium**berghei" >Plasmodium berghei</option>
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82 <option value="Plasmodium**chabaudi" >Plasmodium chabaudi</option>
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83 <option value="Plasmodium**knowlesi" >Plasmodium knowlesi</option>
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84 <option value="Toxoplasma**gondii" >Toxoplasma gondii</option>
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85 <option value="Neospora**caninum" >Neospora caninum</option>
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86 <option value="Trichomonas**vaginalis" >Trichomonas vaginalis</option>
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87 <option value="Trypanosoma**cruzi" >Trypanosoma cruzi</option>
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88 <option value="Leishmania**braziliensis" >Leishmania braziliensis</option>
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89 <option value="Leishmania**infantum" >Leishmania infantum</option>
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90 <option value="Leishmania**major" >Leishmania major</option>
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91 <option value="Leishmania**mexicana" >Leishmania mexicana</option>
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92 <option value="Trypanosoma**brucei" >Trypanosoma brucei</option>
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93 <option value="Trypanosoma**congolense" >Trypanosoma congolense</option>
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94 <option value="Trypanosoma**vivax" >Trypanosoma vivax</option>
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95 </param>
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96 </when>
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97 <when value="cached">
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98 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter Organism"/>
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99 </when></conditional><conditional name="source1">
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100 <param name="source1_source" type="select" label="Min Molecular Weight (Daltons) Source">
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101 <option value="cached" selected="true">Param value will be taken from previous step</option>
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102 <option value="user">User will enter the param value</option>
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103 </param>
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104 <when value="user">
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105 <param format="text" size = "150" name = "user_param1" type="text" label="Enter Min Molecular Weight (Daltons)" help="see tip below" />
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106 </when>
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107 <when value="cached">
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108 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter Min Molecular Weight (Daltons)"/>
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109 </when></conditional><conditional name="source2">
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110 <param name="source2_source" type="select" label="Max Molecular Weight (Daltons) Source">
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111 <option value="cached" selected="true">Param value will be taken from previous step</option>
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112 <option value="user">User will enter the param value</option>
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113 </param>
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114 <when value="user">
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115 <param format="text" size = "150" name = "user_param2" type="text" label="Enter Max Molecular Weight (Daltons)" help="see tip below" />
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116 </when>
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117 <when value="cached">
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118 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter Max Molecular Weight (Daltons)"/>
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119 </when></conditional> <conditional name="cond_source">
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120 <param name="optional_param_source" type="select" label="Display Additional Parameters">
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121 <option value="no" selected="true">no</option>
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122 <option value="yes">yes</option>
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123 </param>
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124 <when value="no">
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125 </when>
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126 <when value="yes">
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127
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128 <conditional name="source3">
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129 <param name="source3_source" type="select" label="Output Fields Source">
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130 <option value="cached" selected="true">Param value will be taken from previous step</option>
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131 <option value="user">User will enter the param value</option>
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132 </param>
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133 <when value="user"><param name="user_param3" type="select" label="Select Output Fields" help="see tip below">
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134 <option value="all" >all</option>
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135 <option value="none" selected="true">none</option>
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136 <option value="primary_key" >primary_key</option>
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137 <option value="formatted_gene_id" >formatted_gene_id</option>
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138 <option value="external_db_name" >external_db_name</option>
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139 <option value="sequence_id" >sequence_id</option>
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140 <option value="chromosome" >chromosome</option>
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141 <option value="location_text" >location_text</option>
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142 <option value="strand" >strand</option>
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143 <option value="gene_type" >gene_type</option>
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144 <option value="exon_count" >exon_count</option>
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145 <option value="transcript_length" >transcript_length</option>
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146 <option value="cds_length" >cds_length</option>
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147 <option value="product" >product</option>
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148 <option value="protein_length" >protein_length</option>
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149 <option value="tm_count" >tm_count</option>
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150 <option value="molecular_weight" >molecular_weight</option>
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151 <option value="isoelectric_point" >isoelectric_point</option>
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152 <option value="ec_numbers_string" >ec_numbers_string</option>
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153 <option value="ortholog_number" >ortholog_number</option>
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154 <option value="paralog_number" >paralog_number</option>
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155 <option value="orthomcl_name" >orthomcl_name</option>
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156 <option value="signalp_scores" >signalp_scores</option>
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157 <option value="signalp_peptide" >signalp_peptide</option>
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158 <option value="ann_go_function" >ann_go_function</option>
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159 <option value="ann_go_process" >ann_go_process</option>
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160 <option value="ann_go_component" >ann_go_component</option>
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161 <option value="pred_go_function" >pred_go_function</option>
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162 <option value="pred_go_process" >pred_go_process</option>
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163 <option value="pred_go_component" >pred_go_component</option>
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164 <option value="organism" >organism</option>
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165 <option value="protein_sequence" >protein_sequence</option>
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166 <option value="transcript_sequence" >transcript_sequence</option>
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167 <option value="cds" >cds</option>
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168 <option value="wdk_weight" >wdk_weight</option>
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169 </param>
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170 </when>
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171 <when value="cached">
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172 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter Output Fields"/>
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173 </when></conditional>
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174
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175 <conditional name="source4">
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176 <param name="source4_source" type="select" label="Output Tables Source">
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177 <option value="cached" selected="true">Param value will be taken from previous step</option>
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178 <option value="user">User will enter the param value</option>
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179 </param>
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180 <when value="user"><param name="user_param4" type="select" label="Select Output Tables" help="see tip below">
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181 <option value="all" >all</option>
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182 <option value="none" selected="true">none</option>
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183 <option value="SNPs" >SNPs</option>
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184 <option value="GeneModelDump" >GeneModelDump</option>
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185 <option value="InterPro" >InterPro</option>
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186 <option value="TMHMM" >TMHMM</option>
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187 <option value="LowComplexity" >LowComplexity</option>
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188 <option value="SignalP" >SignalP</option>
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189 <option value="BlastP" >BlastP</option>
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190 <option value="Genbank" >Genbank</option>
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191 <option value="SageTags" >SageTags</option>
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192 <option value="Notes" >Notes</option>
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193 <option value="UserComments" >UserComments</option>
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194 <option value="CommunityExpComments" >CommunityExpComments</option>
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195 <option value="EcNumber" >EcNumber</option>
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196 <option value="MassSpec" >MassSpec</option>
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197 <option value="GoTerms" >GoTerms</option>
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198 <option value="Aliases" >Aliases</option>
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199 <option value="Phenotype" >Phenotype</option>
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200 <option value="Y2hInteractions" >Y2hInteractions</option>
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201 <option value="Orthologs" >Orthologs</option>
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202 <option value="MetabolicPathways" >MetabolicPathways</option>
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203 <option value="TaskComments" >TaskComments</option>
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204 <option value="ArrayElements" >ArrayElements</option>
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205 <option value="TwoChannelDiffExpr" >TwoChannelDiffExpr</option>
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206 <option value="ProteinExpression" >ProteinExpression</option>
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207 <option value="Mr4Reagents" >Mr4Reagents</option>
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208 <option value="ProteinDatabase" >ProteinDatabase</option>
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209 <option value="GeneLinkouts" >GeneLinkouts</option>
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210 <option value="3dPreds" >3dPreds</option>
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211 <option value="PdbSimilarities" >PdbSimilarities</option>
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212 <option value="Epitopes" >Epitopes</option>
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213 <option value="IsolateOverlap" >IsolateOverlap</option>
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214 </param>
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215 </when>
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216 <when value="cached">
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217 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter Output Tables"/>
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218 </when></conditional>
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219 </when>
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220 </conditional>
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221 </inputs>
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222 <outputs>
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223 <data format="tabular" name="output" />
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224 </outputs>
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225 <help>
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226
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227 .. class:: infomark
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228
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229 **TIP:** Organism type is xsd:string
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230
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231 .. class:: infomark
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232
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233 **TIP:** Min Molecular Weight (Daltons) type is xsd:string
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234
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235 .. class:: infomark
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236
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237 **TIP:** Max Molecular Weight (Daltons) type is xsd:string
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238 </help>
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239 </tool>
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