Mercurial > repos > nick > duplex
comparison make_families.xml @ 2:ba2a53b970ca draft
planemo upload commit 670b3282d2c120882b956ad617e61369467fb0fe
| author | nick |
|---|---|
| date | Tue, 24 Nov 2015 21:22:29 -0500 |
| parents | b63d6673f883 |
| children | 7f513b9b1b1e |
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| 1:b63d6673f883 | 2:ba2a53b970ca |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="make_families" name="Make families" version="0.2"> | 2 <tool id="make_families" name="Du Novo: Make families" version="0.2"> |
| 3 <description>from duplex sequencing data</description> | 3 <description>of duplex sequencing reads</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="0.2">duplex</requirement> | 5 <requirement type="package" version="0.2">duplex</requirement> |
| 6 <requirement type="set_environment">DUPLEX_DIR</requirement> | 6 <requirement type="set_environment">DUPLEX_DIR</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <!-- TODO: Add dependency on coreutils to get paste? --> | |
| 8 <command>paste $fastq1 $fastq2 | 9 <command>paste $fastq1 $fastq2 |
| 9 | paste - - - - | 10 | paste - - - - |
| 10 | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant | 11 | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant |
| 11 | sort | 12 | sort |
| 12 > $output | 13 > $output |