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1 <?xml version='1.1' encoding='utf-8'?>
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2 <tool id="Test-input-into-file" name="Test-File" version="1.0.0" force_history_refresh="True">
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3 <description> Read xml params into a file</description>
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4
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5 <command interpreter="python">Test-input-into-file.py $inputfile "$__tool_dir__" $outputfile
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6 #for $op in $test_param1
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7 ${op.discrete_fields1.Text_Fields1}
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8 #end for
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9 "$EndofVarParam1"
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10 "$Covariate_Type"
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11 "$EndofVarParam2"
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12 #for $op in $test_param3
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13 ${op.discrete_fields3.Text_Fields3}
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14 #end for
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15 "$EndofVarParam3"
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16 </command>
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17 <!-- #in=$__tool_dir__/$inputfile
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18 #inputfile="$__tool_dir__"$inputfile
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19
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20 type Describes the parameter type - each different type as different semantics
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21 and the tool form widget is different. Currently valid parameter types are:
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22 text, integer, float, boolean, genomebuild, select, color, data_column, hidden, hidden_data, baseurl, file, ftpfile, data, data_collection, library_data, drill_down. The definition of supported parameter
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23 types as defined in the parameter_types dictionary in /lib/galaxy/tools/parameters/basic.py.
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24 -->
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25 <stdio>
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26 <exit_code range="1:" level="fatal" />
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27 </stdio>
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28 <inputs>
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29 <data format="txt" name="inputfile"/>
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30 <repeat name="test_param1" title="Select 1 or more Covariate Clinical Categories">
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31 <conditional name="discrete_fields1">
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32 <param name="Text_Fields1" type="select" label="Covariate Bar Choices" help="">
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33 <option value='cat_EMPTY' selected="true">Click cursor in middle of this text to see choices</option>
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34 <option value='cat_SampleTypeCode'>Sample Cohort</option>
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35 <option value='cat_gender'>Gender</option>
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36 <option value='cat_race'>Race</option>
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37 </param>
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38 </conditional>
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39 </repeat>
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40 <param name="EndofVarParam1" type="hidden" value="paramend1" </param>
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41 <param name="Covariate_Type" type="select" value="" label="Type of Covariate Bars" help="Choose Sample or Gene covariate bar files">
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42 <option value="S" selected="true">Participant-Sample</option>
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43 <option value="G" >Gene</option>
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44 </param>
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45 <param name="EndofVarParam2" type="hidden" value="paramend2" </param>
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46 <repeat name="test_param3" title="Select 1 or more Covariate Clinical Categories">
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47 <conditional name="discrete_fields3">
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48 <param name="Text_Fields3" type="select" label="Covariate Bar Choices" help="">
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49 <option value='cat_EMPTY' selected="true">Click cursor in middle of this text to see choices</option>
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50 <option value='cat_SampleTypeCode'>Sample Cohort</option>
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51 <option value='cat_gender'>Gender</option>
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52 <option value='cat_race'>Race</option>
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53 </param>
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54 </conditional>
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55 </repeat>
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56 <param name="EndofVarParam3" type="hidden" value="paramend1" </param>
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57 </inputs>
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58 <outputs>
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59 <data format="txt" name="outputfile" label="${tool.name} on ${on_string}"/>
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60 </outputs>
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61 </tool>
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