Mercurial > repos > petr-novak > re_utils
comparison renameSequences.xml @ 9:c2c69c6090f0 draft
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| author | petr-novak |
|---|---|
| date | Fri, 31 Jan 2020 06:55:23 -0500 |
| parents | e320ef2d105a |
| children | 58807b35777a |
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| 8:99569eccc583 | 9:c2c69c6090f0 |
|---|---|
| 3 <command interpreter="python"> | 3 <command interpreter="python"> |
| 4 renameSequences2.py $input $paired index.tmp $prefix_length > $output | 4 renameSequences2.py $input $paired index.tmp $prefix_length > $output |
| 5 </command> | 5 </command> |
| 6 | 6 |
| 7 <inputs> | 7 <inputs> |
| 8 <param format="fasta" type="data" name="input" label="Choose your fasta file" /> | 8 <param format="fasta" type="data" name="input" label="Choose your FASTA file" /> |
| 9 <param name="prefix_length" type="integer" size="10" value="0" label="Prefix length" help="Enter length of prefix to keep in sequences names" /> | 9 <param name="prefix_length" type="integer" size="10" value="0" label="Prefix length" help="Enter the length of prefix to keep in sequences names" /> |
| 10 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="All sequence reads are paired" help="check if you are using pair reads and input sequences contain both read mates and left mates alternate with their right mates"/> | 10 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequences are paired-end reads in interlaced format" help=""/> |
| 11 </inputs> | 11 </inputs> |
| 12 | 12 |
| 13 | 13 |
| 14 <outputs> | 14 <outputs> |
| 15 <data format="fasta" name="output" label="renamed sequences from dataset ${input.hid}" /> | 15 <data format="fasta" name="output" label="Renamed sequences from dataset ${input.hid}" /> |
| 16 </outputs> | 16 </outputs> |
| 17 | 17 |
| 18 <help> | 18 <help> |
| 19 **What is does** | 19 **What is does** |
| 20 | 20 |
| 21 Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name. | 21 Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name. |
| 22 If paired sequences are used, last character in sequence name is used to distinguish pairs. | 22 If paired-end reads are used, the last character in sequence name is used to distinguish pairs. |
| 23 | 23 |
| 24 </help> | 24 </help> |
| 25 </tool> | 25 </tool> |