Mercurial > repos > jjohnson > fastq_sync
comparison pe_sync.xml @ 0:751f4938cf0d
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| author | jjohnson |
|---|---|
| date | Tue, 05 Feb 2013 15:23:18 -0500 |
| parents | |
| children | b0ab279b5add |
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| -1:000000000000 | 0:751f4938cf0d |
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| 1 <tool id="pe_sync" name="pe-sync: Paired-end synchronization check" version="1.0"> | |
| 2 <description>The Paired-end synchronization check program determines if the reads in paired-end fastq files are in the proper order (synchronized).</description> | |
| 3 <command interpreter="perl"> | |
| 4 pe_sync_2_files.pl $quickcheck $input1 $input2 2>&1 | tee $output | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="input1" type="data" format="fastq" label="Input 1"/> | |
| 8 <param name="input2" type="data" format="fastq" label="Input 2"/> | |
| 9 <param name="quickcheck" type="boolean" truevalue="quick" falsevalue="" checked="false" label="Just check a sample of the sequences" | |
| 10 help=""/> | |
| 11 </inputs> | |
| 12 <stdio> | |
| 13 <exit_code range="1:" level="fatal" description="Bad input dataset" /> | |
| 14 </stdio> | |
| 15 <outputs> | |
| 16 <data format="txt" name="output" label="pe-sync report for ${input1.name} and ${input2.name}"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <help> | |
| 23 Paired-end read file synchronization checks if left and right reads are in the same order. | |
| 24 | |
| 25 The "quick" option will not report the percent of out-of-sync reads | |
| 26 for many failed files, but will run much faster. | |
| 27 | |
| 28 This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids. | |
| 29 Other types of read ID formats may cause a terminal error. | |
| 30 | |
| 31 </help> | |
| 32 </tool> |