[3] | 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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