Mercurial > repos > dfornika > snippy
comparison snippy.xml @ 32:3ac93a6e4687 draft default tip
"planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
| author | dfornika |
|---|---|
| date | Sat, 25 Jan 2020 00:50:20 +0000 |
| parents | 20b52007c4dc |
| children |
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| 31:75cfb1377da1 | 32:3ac93a6e4687 |
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| 50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" | 50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" |
| 51 --peil '$fastq_input.fastq_input_interleaved' | 51 --peil '$fastq_input.fastq_input_interleaved' |
| 52 #end if | 52 #end if |
| 53 | 53 |
| 54 #if "outcon" in str($outputs) and $adv.rename_cons | 54 #if "outcon" in str($outputs) and $adv.rename_cons |
| 55 && sed -i 's/>.*/>${dir_name}/' ${dir_name}/snps.consensus.fa | 55 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa' |
| 56 #end if | 56 #end if |
| 57 | 57 |
| 58 && mv ${dir_name} out | 58 && cp -r '${dir_name}' out |
| 59 && tar -czf out.tgz out | 59 && tar -czf out.tgz '${dir_name}' |
| 60 ]]> </command> | 60 ]]> </command> |
| 61 | 61 |
| 62 <inputs> | 62 <inputs> |
| 63 <expand macro="reference_selector" /> | 63 <expand macro="reference_selector" /> |
| 64 <conditional name="fastq_input"> | 64 <conditional name="fastq_input"> |