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1 <tool id="column_select" name="Column Select" version="1">
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2
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3 <description> extract/rearrange columns from a tab-delimited file </description>
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4 <code file="getcolumnnames.py"/>
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5
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6 <command interpreter="bash">
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7 column_extract.sh
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8 $infile
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9 $outputfile
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10 $removeheader
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11 #for $c in $go.columns
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12 ${c.column}
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13 #end for
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14 </command>
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15
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16 <outputs>
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17 <data format="tabular" name="outputfile" label="${sample} Column extract on ${on_string}"/>
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18 </outputs>
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19
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20 <inputs>
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21
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22 <param name="infile" type="data" label="Select file to extract columns from" help="Must be a tab-separated file with a 1-line header"/>
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23 <param name="removeheader" type="boolean" truevalue="Y" falsevalue="N" selected="false" label="Remove header?" help="If selected, any lines starting with # and any empty lines will not be output."/>
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24
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25 <conditional name="go">
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26 <param name="ready" type="select" label="Ready to select columns?" help="Set to NO and back to YES after changing input file">
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27 <option value="no" selected="True">no</option>
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28 <option value="yes">yes</option>
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29 </param>
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30
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31 <when value="yes">
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32 <repeat name="columns" title="Column" min="1">
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33 <!-- <param name="col" type="data_column" data_ref="infile" multiple="False" label="Column from file to output" /> -->
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34 <param name="column" type="select" dynamic_options="get_headers(infile)" multiple="False" label="Select Column" />
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35 </repeat>
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36 </when>
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37 </conditional>
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38
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39 <param name="sample" type="text" value="" label="Sample Name" help="Optional. For file naming purposes only"/>
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40
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41 </inputs>
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42
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43 <help>
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44
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45
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46 **What it does**
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47 Outputs columns of input file in order specified by user. Columns not selected will not be output.
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48
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49 </help>
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50 </tool>
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