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1 <tool id="client_86" name="wublast.run">
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2 <description> Client for operation : run , Web service : wublast.wublast_services </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 wublast.wublast_services run
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11 "_parameters|_sequence"
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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 "_parameters|_stype"
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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 "_parameters|_program"
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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 "_email"
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33 #if $source3.source3_source=="user":
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34 $source3.user_param3
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35 #else:
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36 fileInput
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37 $source3.cached_param3
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38 #end if
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39 "_parameters|_database|_string|$|"
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40 #if $source4.source4_source=="user":
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41 $source4.user_param4
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42 #else:
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43 fileInput
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44 $source4.cached_param4
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45 #end if
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46 #else:
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47 $output
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48 $servicetype
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49 $url
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50 $method
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51 wublast.wublast_services run
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52 "_parameters|_sequence"
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53 #if $source0.source0_source=="user":
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54 $source0.user_param0
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55 #else:
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56 fileInput
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57 $source0.cached_param0
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58 #end if
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59 "_parameters|_stype"
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60 #if $source1.source1_source=="user":
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61 $source1.user_param1
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62 #else:
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63 fileInput
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64 $source1.cached_param1
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65 #end if
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66 "_parameters|_program"
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67 #if $source2.source2_source=="user":
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68 $source2.user_param2
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69 #else:
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70 fileInput
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71 $source2.cached_param2
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72 #end if
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73 "_email"
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74 #if $source3.source3_source=="user":
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75 $source3.user_param3
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76 #else:
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77 fileInput
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78 $source3.cached_param3
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79 #end if
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80 "_parameters|_database|_string|$|"
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81 #if $source4.source4_source=="user":
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82 $source4.user_param4
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83 #else:
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84 fileInput
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85 $source4.cached_param4
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86 #end if
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87 "_parameters|_sensitivity"
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88 #if $cond_source.source5.source5_source=="user":
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89 $cond_source.source5.user_param5
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90 #else:
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91 fileInput
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92 $cond_source.source5.cached_param5
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93 #end if
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94 "_parameters|_topcombon"
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95 #if $cond_source.source6.source6_source=="user":
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96 $cond_source.source6.user_param6
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97 #else:
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98 fileInput
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99 $cond_source.source6.cached_param6
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100 #end if
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101 "_parameters|_filter"
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102 #if $cond_source.source7.source7_source=="user":
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103 $cond_source.source7.user_param7
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104 #else:
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105 fileInput
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106 $cond_source.source7.cached_param7
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107 #end if
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108 "_parameters|_alignments"
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109 #if $cond_source.source8.source8_source=="user":
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110 $cond_source.source8.user_param8
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111 #else:
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112 fileInput
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113 $cond_source.source8.cached_param8
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114 #end if
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115 "_parameters|_scores"
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116 #if $cond_source.source9.source9_source=="user":
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117 $cond_source.source9.user_param9
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118 #else:
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119 fileInput
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120 $cond_source.source9.cached_param9
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121 #end if
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122 "_parameters|_viewfilter"
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123 #if $cond_source.source10.source10_source=="user":
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124 $cond_source.source10.user_param10
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125 #else:
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126 fileInput
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127 $cond_source.source10.cached_param10
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128 #end if
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129 "_parameters|_sort"
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130 #if $cond_source.source11.source11_source=="user":
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131 $cond_source.source11.user_param11
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132 #else:
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133 fileInput
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134 $cond_source.source11.cached_param11
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135 #end if
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136 "_parameters|_strand"
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137 #if $cond_source.source12.source12_source=="user":
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138 $cond_source.source12.user_param12
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139 #else:
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140 fileInput
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141 $cond_source.source12.cached_param12
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142 #end if
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143 "_parameters|_align"
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144 #if $cond_source.source13.source13_source=="user":
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145 $cond_source.source13.user_param13
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146 #else:
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147 fileInput
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148 $cond_source.source13.cached_param13
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149 #end if
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150 "_parameters|_matrix"
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151 #if $cond_source.source14.source14_source=="user":
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152 $cond_source.source14.user_param14
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153 #else:
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154 fileInput
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155 $cond_source.source14.cached_param14
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156 #end if
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157 "_title"
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158 #if $cond_source.source15.source15_source=="user":
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159 $cond_source.source15.user_param15
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160 #else:
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161 fileInput
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162 $cond_source.source15.cached_param15
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163 #end if
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164 "_parameters|_stats"
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165 #if $cond_source.source16.source16_source=="user":
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166 $cond_source.source16.user_param16
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167 #else:
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168 fileInput
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169 $cond_source.source16.cached_param16
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170 #end if
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171 "_parameters|_exp"
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172 #if $cond_source.source17.source17_source=="user":
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173 $cond_source.source17.user_param17
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174 #else:
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175 fileInput
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176 $cond_source.source17.cached_param17
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177 #end if
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178 #end if
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179 </command>
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180 <inputs>
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181 <param name="servicetype" type="hidden" value="SOAP" />
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182 <param name="url" type="hidden" value="http://www.cs.uga.edu/~guttula/wublast.wsdl" />
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183 <param name="method" type="hidden" value="run" />
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184 <conditional name="source0">
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185 <param name="source0_source" type="select" label="sequence Source">
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186 <option value="cached" selected="true">Param value will be taken from previous step</option>
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187 <option value="user">User will enter the param value</option>
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188 </param>
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189 <when value="user">
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190 <param format="text" size = "150" name = "user_param0" type="text" label="Enter sequence" help="see tip below" />
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191 </when>
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192 <when value="cached">
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193 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter sequence"/>
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194 </when>
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195 </conditional><conditional name="source1">
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196 <param name="source1_source" type="select" label="stype Source">
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197 <option value="cached" selected="true">Param value will be taken from previous step</option>
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198 <option value="user">User will enter the param value</option>
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199 </param>
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200 <when value="user">
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201 <param format="text" size = "150" name = "user_param1" type="text" label="Enter stype" help="see tip below" />
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202 </when>
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203 <when value="cached">
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204 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter stype"/>
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205 </when>
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206 </conditional><conditional name="source2">
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207 <param name="source2_source" type="select" label="program Source">
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208 <option value="cached" selected="true">Param value will be taken from previous step</option>
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209 <option value="user">User will enter the param value</option>
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210 </param>
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211 <when value="user">
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212 <param format="text" size = "150" name = "user_param2" type="text" label="Enter program" help="see tip below" />
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213 </when>
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214 <when value="cached">
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215 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter program"/>
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216 </when>
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217 </conditional><conditional name="source3">
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218 <param name="source3_source" type="select" label="email Source">
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219 <option value="cached" selected="true">Param value will be taken from previous step</option>
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220 <option value="user">User will enter the param value</option>
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221 </param>
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222 <when value="user">
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223 <param format="text" size = "150" name = "user_param3" type="text" label="Enter email" help="see tip below" />
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224 </when>
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225 <when value="cached">
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226 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter email"/>
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227 </when>
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228 </conditional><conditional name="source4">
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229 <param name="source4_source" type="select" label="database Source">
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230 <option value="cached" selected="true">Param value will be taken from previous step</option>
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231 <option value="user">User will enter the param value</option>
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232 </param>
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233 <when value="user">
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234 <param format="text" size = "150" name = "user_param4" type="text" label="Enter database" help="see tip below" />
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235 </when>
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236 <when value="cached">
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237 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter database"/>
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238 </when>
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239 </conditional> <conditional name="cond_source">
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240 <param name="optional_param_source" type="select" label="Display Optional Parameters">
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241 <option value="no" selected="true">no</option>
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242 <option value="yes">yes</option>
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243 </param>
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244 <when value="no">
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245 </when>
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246 <when value="yes">
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247
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248 <conditional name="source5">
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249 <param name="source5_source" type="select" label="sensitivity Source">
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250 <option value="cached" selected="true">Param value will be taken from previous step</option>
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251 <option value="user">User will enter the param value</option>
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252 </param>
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253 <when value="user"><param format="text" size = "150" name = "user_param5" type="text" label="Enter sensitivity" help="see tip below" />
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254 </when>
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255 <when value="cached">
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256 <param name = "cached_param5" type="data" label="Choose the step from which to get the parameter sensitivity"/>
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257 </when>
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258 </conditional>
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259
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260 <conditional name="source6">
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261 <param name="source6_source" type="select" label="topcombon Source">
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262 <option value="cached" selected="true">Param value will be taken from previous step</option>
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263 <option value="user">User will enter the param value</option>
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264 </param>
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265 <when value="user"><param format="text" size = "150" name = "user_param6" type="text" label="Enter topcombon" help="see tip below" />
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266 </when>
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267 <when value="cached">
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268 <param name = "cached_param6" type="data" label="Choose the step from which to get the parameter topcombon"/>
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269 </when>
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270 </conditional>
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271
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272 <conditional name="source7">
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273 <param name="source7_source" type="select" label="filter Source">
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274 <option value="cached" selected="true">Param value will be taken from previous step</option>
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275 <option value="user">User will enter the param value</option>
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276 </param>
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277 <when value="user"><param format="text" size = "150" name = "user_param7" type="text" label="Enter filter" help="see tip below" />
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278 </when>
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279 <when value="cached">
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280 <param name = "cached_param7" type="data" label="Choose the step from which to get the parameter filter"/>
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281 </when>
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282 </conditional>
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283
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284 <conditional name="source8">
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285 <param name="source8_source" type="select" label="alignments Source">
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286 <option value="cached" selected="true">Param value will be taken from previous step</option>
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287 <option value="user">User will enter the param value</option>
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288 </param>
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289 <when value="user"><param format="text" size = "150" name = "user_param8" type="text" label="Enter alignments" help="see tip below" />
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290 </when>
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291 <when value="cached">
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292 <param name = "cached_param8" type="data" label="Choose the step from which to get the parameter alignments"/>
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293 </when>
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294 </conditional>
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295
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296 <conditional name="source9">
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297 <param name="source9_source" type="select" label="scores Source">
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298 <option value="cached" selected="true">Param value will be taken from previous step</option>
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299 <option value="user">User will enter the param value</option>
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300 </param>
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301 <when value="user"><param format="text" size = "150" name = "user_param9" type="text" label="Enter scores" help="see tip below" />
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302 </when>
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303 <when value="cached">
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304 <param name = "cached_param9" type="data" label="Choose the step from which to get the parameter scores"/>
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305 </when>
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306 </conditional>
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307
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308 <conditional name="source10">
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309 <param name="source10_source" type="select" label="viewfilter Source">
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310 <option value="cached" selected="true">Param value will be taken from previous step</option>
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311 <option value="user">User will enter the param value</option>
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312 </param>
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313 <when value="user"><param format="text" size = "150" name = "user_param10" type="text" label="Enter viewfilter" help="see tip below" />
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314 </when>
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315 <when value="cached">
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316 <param name = "cached_param10" type="data" label="Choose the step from which to get the parameter viewfilter"/>
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317 </when>
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318 </conditional>
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319
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320 <conditional name="source11">
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321 <param name="source11_source" type="select" label="sort Source">
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322 <option value="cached" selected="true">Param value will be taken from previous step</option>
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323 <option value="user">User will enter the param value</option>
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324 </param>
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325 <when value="user"><param format="text" size = "150" name = "user_param11" type="text" label="Enter sort" help="see tip below" />
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326 </when>
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327 <when value="cached">
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328 <param name = "cached_param11" type="data" label="Choose the step from which to get the parameter sort"/>
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329 </when>
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330 </conditional>
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331
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332 <conditional name="source12">
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333 <param name="source12_source" type="select" label="strand Source">
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334 <option value="cached" selected="true">Param value will be taken from previous step</option>
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335 <option value="user">User will enter the param value</option>
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336 </param>
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337 <when value="user"><param format="text" size = "150" name = "user_param12" type="text" label="Enter strand" help="see tip below" />
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338 </when>
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339 <when value="cached">
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340 <param name = "cached_param12" type="data" label="Choose the step from which to get the parameter strand"/>
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341 </when>
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342 </conditional>
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343
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344 <conditional name="source13">
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345 <param name="source13_source" type="select" label="align Source">
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346 <option value="cached" selected="true">Param value will be taken from previous step</option>
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347 <option value="user">User will enter the param value</option>
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348 </param>
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349 <when value="user"><param format="text" size = "150" name = "user_param13" type="text" label="Enter align" help="see tip below" />
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350 </when>
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351 <when value="cached">
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352 <param name = "cached_param13" type="data" label="Choose the step from which to get the parameter align"/>
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353 </when>
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354 </conditional>
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355
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356 <conditional name="source14">
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357 <param name="source14_source" type="select" label="matrix Source">
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358 <option value="cached" selected="true">Param value will be taken from previous step</option>
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359 <option value="user">User will enter the param value</option>
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360 </param>
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361 <when value="user"><param format="text" size = "150" name = "user_param14" type="text" label="Enter matrix" help="see tip below" />
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362 </when>
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363 <when value="cached">
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364 <param name = "cached_param14" type="data" label="Choose the step from which to get the parameter matrix"/>
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365 </when>
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366 </conditional>
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367
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368 <conditional name="source15">
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369 <param name="source15_source" type="select" label="title Source">
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370 <option value="cached" selected="true">Param value will be taken from previous step</option>
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371 <option value="user">User will enter the param value</option>
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372 </param>
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373 <when value="user"><param format="text" size = "150" name = "user_param15" type="text" label="Enter title" help="see tip below" />
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374 </when>
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375 <when value="cached">
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376 <param name = "cached_param15" type="data" label="Choose the step from which to get the parameter title"/>
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377 </when>
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378 </conditional>
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379
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380 <conditional name="source16">
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381 <param name="source16_source" type="select" label="stats Source">
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382 <option value="cached" selected="true">Param value will be taken from previous step</option>
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383 <option value="user">User will enter the param value</option>
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384 </param>
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385 <when value="user"><param format="text" size = "150" name = "user_param16" type="text" label="Enter stats" help="see tip below" />
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386 </when>
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387 <when value="cached">
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388 <param name = "cached_param16" type="data" label="Choose the step from which to get the parameter stats"/>
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389 </when>
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390 </conditional>
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391
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392 <conditional name="source17">
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393 <param name="source17_source" type="select" label="exp Source">
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394 <option value="cached" selected="true">Param value will be taken from previous step</option>
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395 <option value="user">User will enter the param value</option>
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396 </param>
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397 <when value="user"><param format="text" size = "150" name = "user_param17" type="text" label="Enter exp" help="see tip below" />
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398 </when>
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399 <when value="cached">
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400 <param name = "cached_param17" type="data" label="Choose the step from which to get the parameter exp"/>
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401 </when>
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402 </conditional>
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403 </when>
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404 </conditional>
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405 </inputs>
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406 <outputs>
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407 <data format="tabular" name="output" />
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408 </outputs>
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409 <help>
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410
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411 .. class:: infomark
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412
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413 **TIP:** About sequence: type is String
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414
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415 .. class:: infomark
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416
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417 **TIP:** About stype: type is String
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418
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419 .. class:: infomark
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420
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421 **TIP:** About program: type is String
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422
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423 .. class:: infomark
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424
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425 **TIP:** About email: type is String
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426
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427 .. class:: infomark
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428
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429 **TIP:** About database: type is String
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430 </help>
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431 </tool> |
