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1 <tool id="cshl_join_tool" name="join">
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2 <description>two files</description>
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3 <command interpreter="sh">join_tool.sh "$jointype" "$output_format"
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4 "$empty_string_filler" "$delimiter"
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5 "$ignore_case"
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6 "$input1" "$column1"
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7 "$input2" "$column2"
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8 "$output"
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9 </command>
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10
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11 <inputs>
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12 <param format="txt" name="input1" type="data" label="1st file" />
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13 <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="input1" accept_default="true" />
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14
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15 <param format="txt" name="input2" type="data" label="2nd File" />
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16 <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="input2" accept_default="true" />
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17
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18 <param name="jointype" type="select" label="Output lines appearing in">
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19 <option value=" ">BOTH 1st & 2nd file.</option>
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20 <option value="-v 1">1st but not in 2nd file. [-v 1]</option>
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21 <option value="-v 2">2nd but not in 1st file. [-v 2]</option>
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22 <option value="-a 1">both 1st & 2nd file, plus unpairable lines from 1st file. [-a 1]</option>
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23 <option value="-a 2">both 1st & 2nd file, plus unpairable lines from 2st file. [-a 2]</option>
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24 <option value="-a 1 -a 2">All Lines [-a 1 -a 2]</option>
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25 </param>
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26
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27 <param name="delimiter" type="select" label="field-separator [-t]">
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28 <option value=",">comma (,)</option>
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29 <option value=":">colons (:) </option>
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30 <option value=" ">single space</option>
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31 <option value=".">dot (.)</option>
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32 <option value="-">dash (-)</option>
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33 <option value="|">pipe (|)</option>
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34 <option value="_">underscore (_)</option>
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35 <option selected="True" value="tab">tab</option>
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36 </param>
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37
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38 <param name="ignore_case" type="select" label="Case sensitivity">
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39 <option value="">Case sensitive</option>
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40 <option value="-i">Case INsensitive [-i]</option>
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41 </param>
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42
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43 <param name="empty_string_filler" type="text" size="20" label="String replacement for empty fields [-e EMPTY]" help="Leave empty unless you know what you're doing. Use this when specifing output format" />
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44
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45 <param name="output_format" type="text" size="30" label="Output line format [-o FORMAT]" help="Leave empty unless you know what you're doing. Example: 1.1,2.1,2.1" />
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46
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47 </inputs>
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48 <outputs>
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49 <data name="output" format="input" metadata_source="input1" />
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50 </outputs>
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51
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52 <help>
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53 </help>
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54 </tool>
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