Mercurial > repos > devteam > trimmer
comparison trimmer.xml @ 1:e632b6c79f7b
Added quotes and brackets to appropriate command arguments
| author | greg <greg@bx.psu.edu> |
|---|---|
| date | Mon, 01 Apr 2013 14:08:19 -0400 |
| parents | f862a6e4d096 |
| children | 3983fbf107b6 |
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| 0:f862a6e4d096 | 1:e632b6c79f7b |
|---|---|
| 1 <tool id="trimmer" name="Trim" version="0.0.1"> | 1 <tool id="trimmer" name="Trim" version="0.0.1"> |
| 2 <description>leading or trailing characters</description> | 2 <description>leading or trailing characters</description> |
| 3 <command interpreter="python"> | 3 <command interpreter="python"> |
| 4 trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 | 4 trimmer.py -a -f "${input1}" -c "${col}" -s "${start}" -e "${end}" -i "${ignore}" "${fastq}" > "${out_file1}" |
| 5 </command> | 5 </command> |
| 6 <inputs> | 6 <inputs> |
| 7 <param format="tabular,txt" name="input1" type="data" label="this dataset"/> | 7 <param format="tabular,txt" name="input1" type="data" label="this dataset"/> |
| 8 <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> | 8 <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> |
| 9 <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> | 9 <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> |