Mercurial > repos > rnateam > bctools
comparison flexbar_split_RR_bcs.xml @ 58:bbbae1ee87e0 draft default tip
fix for flexbar with small data issue
author | rnateam |
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date | Tue, 16 Feb 2016 10:08:58 -0500 |
parents | 25ebec14969a |
children |
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57:537657678b2b | 58:bbbae1ee87e0 |
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12 <requirement type="package" version="2.5">flexbar</requirement> | 12 <requirement type="package" version="2.5">flexbar</requirement> |
13 </requirements> | 13 </requirements> |
14 | 14 |
15 <version_command>flexbar --version</version_command> | 15 <version_command>flexbar --version</version_command> |
16 | 16 |
17 <command> | 17 <command><![CDATA[ |
18 | 18 |
19 flexbar | 19 flexbar |
20 | 20 |
21 --threads \${GALAXY_SLOTS:-1} | 21 --threads \${GALAXY_SLOTS:-1} |
22 | 22 |
47 --barcode-threshold $bThresh | 47 --barcode-threshold $bThresh |
48 | 48 |
49 --max-uncalled $maxUncalled | 49 --max-uncalled $maxUncalled |
50 --min-read-length $minReadLen | 50 --min-read-length $minReadLen |
51 | 51 |
52 > $output; | 52 > $output |
53 | 53 |
54 mv flexbar_barcode_repA_1.fastq $output_repA_1; | 54 && mv flexbar_barcode_repA_1.fastq $output_repA_1 |
55 mv flexbar_barcode_repA_2.fastq $output_repA_2; | 55 && mv flexbar_barcode_repA_2.fastq $output_repA_2 |
56 mv flexbar_barcode_repB_1.fastq $output_repB_1; | 56 && mv flexbar_barcode_repB_1.fastq $output_repB_1 |
57 mv flexbar_barcode_repB_2.fastq $output_repB_2; | 57 && mv flexbar_barcode_repB_2.fastq $output_repB_2 |
58 | 58 |
59 </command> | 59 && sleep 20 |
60 | |
61 ]]></command> | |
60 | 62 |
61 | 63 |
62 <inputs> | 64 <inputs> |
63 | 65 |
64 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> | 66 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> |