Mercurial > repos > petr-novak > re_utils
comparison paired_fastq_filtering.xml @ 33:f1738f8649b0 draft
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
| author | petr-novak |
|---|---|
| date | Fri, 04 Aug 2023 08:09:40 +0000 |
| parents | 36c418bca8b2 |
| children |
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| 32:628b235d76c7 | 33:f1738f8649b0 |
|---|---|
| 7 including trimming, quality filtering, cutadapt filtering and interlacing. Broken | 7 including trimming, quality filtering, cutadapt filtering and interlacing. Broken |
| 8 pairs are discarded. | 8 pairs are discarded. |
| 9 </description> | 9 </description> |
| 10 <requirements> | 10 <requirements> |
| 11 <requirement type="package">blast</requirement> | 11 <requirement type="package">blast</requirement> |
| 12 <requirement type="package">cutadapt</requirement> | 12 <requirement type="package" version="4.4">cutadapt</requirement> |
| 13 <requirement type="package">bioconductor-shortread</requirement> | 13 <requirement type="package">bioconductor-shortread</requirement> |
| 14 <requirement type="package">r-optparse</requirement> | 14 <requirement type="package">r-optparse</requirement> |
| 15 </requirements> | 15 </requirements> |
| 16 <required_files> | 16 <required_files> |
| 17 <include type="literal" path="paired_fastq_filtering_wrapper.sh"/> | 17 <include type="literal" path="paired_fastq_filtering_wrapper.sh"/> |
| 18 <include type="literal" path="paired_fastq_filtering.R"/> | 18 <include type="literal" path="paired_fastq_filtering.R"/> |
| 19 <include type="literal" path="fasta_interlacer.py"/> | 19 <include type="literal" path="fasta_interlacer.py"/> |
| 20 </required_files> | 20 </required_files> |
| 21 <command> | 21 <command> |
| 22 cutadapt --version; | |
| 22 bash '$__tool_directory__'/paired_fastq_filtering_wrapper.sh -a ${A} -b ${B} -o | 23 bash '$__tool_directory__'/paired_fastq_filtering_wrapper.sh -a ${A} -b ${B} -o |
| 23 ${paired} -c ${cut_off} -p ${percent_above} -N ${max_n} $rename -G ${png_output} | 24 ${paired} -c ${cut_off} -p ${percent_above} -N ${max_n} $rename -G ${png_output} |
| 24 | 25 |
| 25 #if $sampling.sequence_sampling : | 26 #if $sampling.sequence_sampling : |
| 26 -n $sampling.sample_size | 27 -n $sampling.sample_size |