Mercurial > repos > jjohnson > fastq_sync
comparison resync.xml @ 0:751f4938cf0d
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author | jjohnson |
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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="resync" name="resync: Paired-end resynchronization" version="1.0"> | |
2 <description>Resynchronize a pair of paired-end fastq files</description> | |
3 <command interpreter="perl"> | |
4 resync.pl $input1 $input2 $output1 $output2 | |
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 </inputs> | |
10 <stdio> | |
11 <exit_code range="1:" level="fatal" description="Bad input dataset" /> | |
12 </stdio> | |
13 <outputs> | |
14 <data format_source="input1" name="output1" label="resync ${input1.name}"/> | |
15 <data format_source="input2" name="output2" label="resync ${input2.name}"/> | |
16 </outputs> | |
17 <tests> | |
18 <test> | |
19 </test> | |
20 </tests> | |
21 <help> | |
22 Resynchronize a pair of paired-end fastq files. | |
23 | |
24 Reads in two potentially unsynchronized fastq files and writes out two synchronized fastq files. | |
25 | |
26 This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids. | |
27 Other types of read ID formats may cause a terminal error. | |
28 | |
29 The synchronized files have properly paired reads, with singelton reads removed. | |
30 | |
31 </help> | |
32 </tool> |