Mercurial > repos > nick > dunovo
comparison correct_barcodes.xml @ 5:000969829a5d draft
correct.py wrapper fix
| author | nick |
|---|---|
| date | Fri, 27 Oct 2017 12:50:39 -0400 |
| parents | 5fbeaa41b223 |
| children | 23f5d9316694 |
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| 4:5fbeaa41b223 | 5:000969829a5d |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6"> | 2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6.1"> |
| 3 <description>of duplex sequencing reads</description> | 3 <description>of duplex sequencing reads</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2.2.5">bowtie2</requirement> | 5 <requirement type="package" version="2.2.5">bowtie2</requirement> |
| 6 <requirement type="package" version="0.1.18">samtools</requirement> | 6 <requirement type="package" version="0.1.18">samtools</requirement> |
| 7 <requirement type="package" version="1.11">networkx</requirement> | 7 <requirement type="package" version="1.11">networkx</requirement> |
| 8 <requirement type="package" version="2.0.6">dunovo</requirement> | 8 <requirement type="package" version="2.0.6">dunovo</requirement> |
| 9 <!-- TODO: require Python 2.7 --> | 9 <!-- TODO: require Python 2.7 --> |
| 10 </requirements> | 10 </requirements> |
| 11 <version_command>correct.py --version</version_command> | |
| 11 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
| 12 baralign.sh '$input' refdir | 13 baralign.sh '$input' refdir correct.sam |
| 13 | samtools view -S -f 256 - | 14 && samtools view -S -f 256 correct.sam |
| 14 | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa | 15 | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa |
| 15 | sort | 16 > families.corrected.tsv |
| 16 > '$output' | 17 && sort families.corrected.tsv |
| 18 > '$output' | |
| 17 ]]> | 19 ]]> |
| 18 </command> | 20 </command> |
| 19 <inputs> | 21 <inputs> |
| 20 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> | 22 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
| 21 <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/> | 23 <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/> |