Mercurial > repos > konradpaszkiewicz > preppereadsforveletfasta
comparison preppereads_fasta.xml @ 0:4d237a31970b default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | konradpaszkiewicz |
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| date | Tue, 07 Jun 2011 17:42:21 -0400 |
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| -1:000000000000 | 0:4d237a31970b |
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| 1 <tool id="preppereadsforveletfasta" name="Prepare reads for use with velvet (FASTA)" version="1.0.0"> | |
| 2 <description>Prepare paired-end reads for use with Velvet</description> | |
| 3 <command interpreter="python"> | |
| 4 preppereads_fasta.py | |
| 5 '$__app__.config.new_file_path' | |
| 6 '$input1' | |
| 7 '$input2' | |
| 8 '$outpe' | |
| 9 '$outsingletons'; exit 0 | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="input1" type="data" format="fasta" label="Read 1 of paired-end dataset"/> | |
| 13 <param name="input2" type="data" format="fasta" label="Read 2 of paired-end dataset"/> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="fasta" name="outpe" label="Merged paired-end reads ready for velvet"/> | |
| 17 <data format="fasta" name="outsingletons" label="Singleton reads reads for velvet"/> | |
| 18 | |
| 19 </outputs> | |
| 20 <requirements> | |
| 21 </requirements> | |
| 22 <help> | |
| 23 **Paired-end reads preparation for velvet** | |
| 24 | |
| 25 Velvet requires paired-end reads to be in the same file in an interleaved FASTQ format. This format specifies that read 1 should be followed immediately by read 2. | |
| 26 | |
| 27 This script is useful to ensure reads are in the correct order prior to passing the data to Velvet. | |
| 28 | |
| 29 Singleton reads can also be produced if quality trimming or other filtering criteria have removed the read's mate. These can also be passed to Velvet using a second short read channel. | |
| 30 | |
| 31 </help> | |
| 32 </tool> |