Mercurial > repos > devteam > trimmer
comparison trimmer.xml @ 2:3983fbf107b6 draft default tip
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 15:49:26 -0400 |
| parents | e632b6c79f7b |
| children |
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| 1:e632b6c79f7b | 2:3983fbf107b6 |
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| 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" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> |
| 10 <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> | 10 <param name="end" type="integer" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> |
| 11 <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> | 11 <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> |
| 12 <option selected="true" value="">No</option> | 12 <option selected="true" value="">No</option> |
| 13 <option value="-q">Yes</option> | 13 <option value="-q">Yes</option> |
| 14 </param> | 14 </param> |
| 15 <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> | 15 <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> |