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1 <tool id="chr_prefix" name="Add/Remove chr prefix" version="1">
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2
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3 <description> add or remove chr prefix from a column </description>
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4
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5 <code file="getcolumnnames.py"/>
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6
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7 <command interpreter="bash">
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8 chrprefix.sh
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9 $infile
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10 "${go.column}"
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11 $addremove
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12 $outputfile
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13 </command>
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14
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15 <outputs>
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16 <data format="tabular" name="outputfile" label="${sample} - chr-prefix on ${on_string}"/>
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17 </outputs>
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18
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19 <inputs>
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20
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21 <param name="infile" type="data" label="Select inputfile" help="must be a tab-delimited file with a 1-line header" />
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22 <conditional name="go">
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23 <param name="ready" type="select" label="Ready to select column?" help="Set to NO and back to YES after changing input file">
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24 <option value="no" selected="True">no</option>
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25 <option value="yes">yes</option>
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26 </param>
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27
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28 <when value="yes">
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29 <param name="column" type="select" dynamic_options="get_headers(infile)" multiple="False" label="Select Column" />
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30 </when>
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31 </conditional>
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32
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33 <param name="addremove" type="select" label="Add or remove the chr prefix?">
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34 <option value="add">Add</option>
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35 <option value="remove">Remove</option>
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36 </param>
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37 <param name="sample" type="text" value="" label="Output File Name" help="Optional."/>
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38
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39 </inputs>
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40
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41 <help>
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42
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43 **What it does**
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44 removes or adds the "chr" prefix in a column of a file. Some tools expect you to indicate chromosomes as "chr1,chr2,chrX", while others expect only 1,2,X as input. This tool allows you to easily switch notations
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45
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46 </help>
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47 </tool>
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