Mercurial > repos > iuc > map_param_value

annotate map_param_value.xml @ 1:a01f088d0e5e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
author iuc
date Wed, 19 Oct 2022 11:37:19 +0000
parents 43d7b3642a30
children 5ac8a4bf7a8d
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a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
iuc
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1 <tool name="Map parameter value" id="map_param_value" version="0.1.1" tool_type="expression" profile="22.01">
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2 <macros>
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3 <xml name="when_element" tokens="type_selection">
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4 <param name="input_param" type="@TYPE_SELECTION@" optional="true" label="Value to map">
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
iuc
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5 <sanitizer sanitize="false"/>
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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6 </param>
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7 <repeat name="mappings" label="Add value mapping">
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8 <param name="from" type="@TYPE_SELECTION@" optional="true" label="Map from this value">
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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9 <sanitizer sanitize="false"/>
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10 </param>
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11 <param name="to" type="text" optional="true" label="to this value" help="This value must be coercable to the selected output parameter type">
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
iuc
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12 <sanitizer sanitize="false"/>
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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13 </param>
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14 </repeat>
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15 </xml>
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16 </macros>
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17 <expression type="ecma5.1">
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18 <![CDATA[{
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19 const source = $job.input_param_type.input_param;
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20 const mappings = $job.input_param_type.mappings;
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21
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22 const coerceToOutput = function(value) {
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23 switch($job.output_param_type) {
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24 case "integer":
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25 return parseInt(value)
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26 case "float":
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27 return parseFloat(value)
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28 case "boolean":
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29 if (value == "false" || value == "False") {
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30 return false
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31 }
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32 return !!value
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33 case "text":
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34 return value
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35 }
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36 }
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37
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38 for ( var i = 0; i < mappings.length; i++ ) {
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39 if ( String(mappings[i].from) == String(source) ) {
0
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40 return { output: coerceToOutput(mappings[i].to) };
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41 }
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42 }
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43 if ( $job.unmapped.on_unmapped == "fail" ) {
1
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44 return { __error_message: `input_param ${source} not found in mapping values.` };
0
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45 } else if ( $job.unmapped.on_unmapped == "default" ) {
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46 return { output: coerceToOutput($job.unmapped.default_value) };
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47 }
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48 return { output: coerceToOutput(source) };
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49 }]]>
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50 </expression>
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51 <inputs>
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52 <conditional name="input_param_type">
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53 <param name="type" type="select" label="Select type of input parameter to match">
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54 <option value="text" selected="true">Text</option>
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55 <option value="integer">Integer</option>
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56 <option value="float">Float</option>
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57 <option value="boolean">Boolean</option>
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58 </param>
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59 <when value="text">
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60 <expand macro="when_element" type_selection="text"/>
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61 </when>
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62 <when value="integer">
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63 <expand macro="when_element" type_selection="integer"/>
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64 </when>
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65 <when value="float">
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66 <expand macro="when_element" type_selection="float"/>
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67 </when>
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68 <when value="boolean">
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69 <expand macro="when_element" type_selection="boolean"/>
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70 </when>
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71 </conditional>
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72 <conditional name="unmapped">
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73 <param name="on_unmapped" type="select" label="Select how to handle unmapped values">
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74 <option value="input">Use unmodified input parameter value if input parameter value not found in mappings</option>
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75 <option value="fail">Fail if input parameter value not found in mappings</option>
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76 <option value="default">Provide a default value to use if input parameter value not found in mappings</option>
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77 </param>
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78 <when value="input" />
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79 <when value="fail" />
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80 <when value="default">
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81 <param name="default_value" type="text" label="Use this value if the input parameter value was not found in mappings"/>
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82 </when>
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83 </conditional>
1
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84 <param name="output_param_type" type="select" label="Select type of parameter to output">
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85 <option value="text">Text</option>
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86 <option value="integer">Integer</option>
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87 <option value="float">Float</option>
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88 <option value="boolean">Boolean</option>
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89 </param>
0
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90 </inputs>
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91 <outputs>
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92 <output type="text" name="output_param_text" from="output">
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93 <filter>output_param_type == 'text'</filter>
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94 </output>
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95 <output type="integer" name="output_param_integer" from="output">
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96 <filter>output_param_type == 'integer'</filter>
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97 </output>
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98 <output type="float" name="output_param_float" from="output">
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99 <filter>output_param_type == 'float'</filter>
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100 </output>
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101 <output type="boolean" name="output_param_boolean" from="output">
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102 <filter>output_param_type == 'boolean'</filter>
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103 </output>
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104 </outputs>
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105 <tests>
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106 <test expect_num_outputs="1">
1
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107 <!-- map string A to string B -->
0
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108 <conditional name="input_param_type">
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109 <param name="type" value="text"/>
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110 <param name="input_param" value="A" />
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111 <repeat name="mappings">
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112 <param name="from" value="A" />
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113 <param name="to" value="B" />
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114 </repeat>
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115 </conditional>
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116 <output name="output_param_text" value_json="&quot;B&quot;" />
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117 </test>
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118 <test expect_num_outputs="1">
1
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119 <!-- test that mapping works in the presence of usually sanitized characters -->
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120 <conditional name="input_param_type">
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121 <param name="type" value="text"/>
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122 <param name="input_param" value="echo $abc &gt; 1" />
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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123 <repeat name="mappings">
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124 <param name="from" value="echo $abc &gt; 1" />
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125 <param name="to" value="echo $abc &gt; 2" />
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126 </repeat>
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127 </conditional>
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128 <output name="output_param_text" value_json="&quot;echo $abc &gt; 2&quot;" />
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129 </test>
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130 <test expect_num_outputs="1">
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131 <!-- keep unmodified input if no match in mapping values -->
0
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132 <conditional name="input_param_type">
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133 <param name="input_param" value="C" />
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134 <repeat name="mappings">
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135 <param name="from" value="A" />
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136 <param name="to" value="B" />
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137 </repeat>
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138 </conditional>
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139 <output name="output_param_text" value_json="&quot;C&quot;" />
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140 </test>
1
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141 <test expect_failure="true">
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142 <!-- fail job if no mapping found and on_unmapped is set to fail -->
0
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143 <conditional name="input_param_type">
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144 <param name="input_param" value="C" />
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145 <repeat name="mappings">
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146 <param name="from" value="A" />
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147 <param name="to" value="B" />
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148 </repeat>
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149 </conditional>
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150 <conditional name="unmapped">
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151 <param name="on_unmapped" value="fail"/>
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152 </conditional>
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153 </test>
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154 <test expect_num_outputs="1">
1
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155 <!-- map unspecified option text to string default via unmapped default value -->
0
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156 <conditional name="input_param_type">
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157 <repeat name="mappings">
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158 <param name="from" value="A" />
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159 <param name="to" value="B" />
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160 </repeat>
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161 </conditional>
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162 <conditional name="unmapped">
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163 <param name="on_unmapped" value="default"/>
1
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164 <param name="default_value" value="default"/>
0
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165 </conditional>
1
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166 <output name="output_param_text" value_json="&quot;default&quot;" />
0
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167 </test>
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168 <test expect_num_outputs="1">
1
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169 <!-- map string C to string X via default value -->
0
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170 <conditional name="input_param_type">
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171 <param name="input_param" value="C" />
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172 <repeat name="mappings">
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173 <param name="from" value="A" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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174 <param name="to" value="B" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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175 </repeat>
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176 </conditional>
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177 <conditional name="unmapped">
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178 <param name="on_unmapped" value="default"/>
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179 <param name="default_value" value="X"/>
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180 </conditional>
1
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181 <output name="output_param_text" value_json="&quot;X&quot;" />
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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182 </test>
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183 <test expect_num_outputs="1">
1
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184 <!-- map string C to string D in presence of multiple mappings -->
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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185 <conditional name="input_param_type">
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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186 <param name="input_param" value="C" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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187 <repeat name="mappings">
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188 <param name="from" value="A" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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189 <param name="to" value="B" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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190 </repeat>
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191 <repeat name="mappings">
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192 <param name="from" value="C" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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193 <param name="to" value="D" />
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194 </repeat>
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195 </conditional>
1
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196 <output name="output_param_text" value_json="&quot;D&quot;" />
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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197 </test>
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198 <test expect_num_outputs="1">
1
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199 <!-- map integer 42 to integer true value -->
0
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200 <conditional name="input_param_type">
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201 <param name="type" value="integer" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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202 <param name="input_param" value="42" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
iuc
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203 <repeat name="mappings">
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204 <param name="from" value="42" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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205 <param name="to" value="true" />
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206 </repeat>
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207 </conditional>
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208 <param name="output_param_type" value="boolean"/>
1
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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209 <output name="output_param_boolean" value_json="true" />
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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210 </test>
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211 <test expect_num_outputs="1">
1
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212 <!-- map float 1.2 to boolean false via unmapped default value -->
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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213 <conditional name="input_param_type">
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214 <param name="type" value="float" />
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215 <param name="input_param" value="1.2" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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216 <repeat name="mappings">
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217 <param name="from" value="42" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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218 <param name="to" value="true" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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219 </repeat>
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220 </conditional>
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221 <conditional name="unmapped">
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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222 <param name="on_unmapped" value="default"/>
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223 <param name="default_value" value="False"/>
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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224 </conditional>
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225 <param name="output_param_type" value="boolean"/>
1
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226 <output name="output_param_boolean" value_json="false" />
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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227 </test>
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228 <test expect_num_outputs="1">
1
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229 <!-- map integer 1 to float 1.1 -->
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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230 <conditional name="input_param_type">
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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231 <param name="type" value="integer" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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232 <param name="input_param" value="1" />
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233 <repeat name="mappings">
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234 <param name="from" value="1" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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235 <param name="to" value="1.1" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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236 </repeat>
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237 </conditional>
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238 <param name="output_param_type" value="float"/>
1
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239 <output name="output_param_float" value_json="1.1" />
0
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240 </test>
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241 <test expect_num_outputs="1">
1
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242 <!-- map string A to integer 2 -->
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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243 <conditional name="input_param_type">
1
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244 <param name="type" value="text" />
0
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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245 <param name="input_param" value="A" />
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246 <repeat name="mappings">
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247 <param name="from" value="A" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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248 <param name="to" value="2" />
43d7b3642a30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 9cbf1d6cb6a59b8b4172d09449aac695ba10687d
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249 </repeat>
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250 </conditional>
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251 <param name="output_param_type" value="integer"/>
1
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252 <output name="output_param_integer" value_json="2" />
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253 </test>
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254 <test expect_num_outputs="1">A
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255 <!-- map string False to boolean false -->
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256 <conditional name="input_param_type">
a01f088d0e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
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257 <param name="type" value="text" />
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258 <param name="input_param" value="False" />
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259 <repeat name="mappings">
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260 <param name="from" value="False" />
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261 <param name="to" value="false" />
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262 </repeat>
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263 </conditional>
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264 <conditional name="unmapped">
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265 <param name="on_unmapped" value="fail"/>
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266 </conditional>
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267 <param name="output_param_type" value="boolean"/>
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268 <output name="output_param_boolean" value_json="false" />
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269 </test>
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270 <test expect_num_outputs="1">
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271 <!-- map boolean false to boolean true -->
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272 <conditional name="input_param_type">
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273 <param name="type" value="boolean" />
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274 <param name="input_param" value="false" />
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275 <repeat name="mappings">
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276 <param name="from" value="false" />
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277 <param name="to" value="true" />
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278 </repeat>
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279 </conditional>
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280 <conditional name="unmapped">
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281 <param name="on_unmapped" value="fail"/>
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282 </conditional>
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283 <param name="output_param_type" value="boolean"/>
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284 <output name="output_param_boolean" value_json="true" />
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285 </test>
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286 <test expect_num_outputs="1">
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287 <!-- map integer 0 to boolean false via default value coercion -->
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288 <conditional name="input_param_type">
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289 <param name="type" value="integer" />
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290 <param name="input_param" value="0" />
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291 </conditional>
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292 <param name="output_param_type" value="boolean"/>
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293 <output name="output_param_boolean" value_json="false" />
0
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294 </test>
1
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295 <test expect_num_outputs="1">
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296 <!-- map null text value to boolean true -->
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297 <conditional name="input_param_type">
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298 <param name="type" value="text" />
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299 <param name="input_param" value_json="null" />
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300 <repeat name="mappings">
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301 <param name="from" value_json="null" />
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302 <param name="to" value="true" />
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303 </repeat>
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304 </conditional>
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305 <param name="output_param_type" value="boolean"/>
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306 <output name="output_param_boolean" value_json="true" />
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307 </test>
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308 <test expect_num_outputs="1" doc="map null integer value to boolean true">
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309 <!-- map null integer value to boolean true -->
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310 <conditional name="input_param_type">
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311 <param name="type" value="integer" />
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312 <param name="input_param" value_json="null" />
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313 <repeat name="mappings">
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314 <param name="from" value_json="null" />
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315 <param name="to" value="true" />
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316 </repeat>
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317 </conditional>
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318 <param name="output_param_type" value="boolean"/>
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319 <output name="output_param_boolean" value_json="true" />
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320 </test>
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321 <test expect_num_outputs="1">
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322 <!-- map integer value to null text -->
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323 <conditional name="input_param_type">
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324 <param name="type" value="integer" />
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325 <param name="input_param" value="1" />
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326 <repeat name="mappings">
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327 <param name="from" value="1" />
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328 <param name="to" value_json="null" />
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329 </repeat>
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330 </conditional>
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331 <param name="output_param_type" value="text"/>
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332 <output name="output_param_text" value_json="null" />
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333 </test>
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334 <!-- Old Galaxy issue, optional unset text input still recorded as ""
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335 We could work around this with a conditional, but no usecase yet
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336 and we should better fix this in Galaxy
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337 <test expect_num_outputs="1">
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338 <conditional name="input_param_type">
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339 <param name="input_param" value="A" />
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340 <repeat name="mappings">
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341 <param name="from" value="A" />
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342 </repeat>
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343 </conditional>
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344 <output name="output_param_text" value_json="null" />
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345 </test>
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346 -->
0
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347 </tests>
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348 <help><![CDATA[
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349 **What it does**
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350
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351 Maps a parameter value to another value.
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352 This can be used to transform any non-data value (text, integer, float and boolean) to a different value of a different type.
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353
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354 **Settings**
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355
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356 If the value is not found in the mapping the unmodified value is returned by default.
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357 Select ``Fail if input parameter value not found in mappings`` if you wish the job to fail if an input could not be mapped.
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358
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359 Select ``Provide a default value to use if input parameter value not found in mappings`` to provide a default value to use in case the input parameter value could not be mapped.
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360 Select the proper input and output parameter types based on your workflow input and output connections.
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361
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362 **Examples**
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363
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364 You want a user to select from 3 simple options in a workflow, e.g. ``low``, ``medium``, ``high``, which correspond to distinct integer values.
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365
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366 Turn ``Map this parameter value to a different value`` into a a connectable workflow input by clicking on "Add connection to module".
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367
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368 Set the input parameter type to ``Text``, and add 3 mappings:
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369
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370 ..
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371
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372 #.
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373
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374 * Map from this value: ``low``
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375 * to this value: ``1``
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376
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377 #.
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378
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379 * Map from this value: ``medium``
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380 * to this value: ``2``
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381
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382 #.
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383
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384 * Map from this value: ``high``
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385 * to this value: ``3``
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386
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387 Set ``Select type of parameter to output`` to ``Integer``.
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388 You can now connect the output to any connectable Integer input in your workflow.
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389
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390 ]]></help>
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391 </tool>