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comparison single_fastq_filtering.xml @ 33:f1738f8649b0 draft

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planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
author petr-novak
date Fri, 04 Aug 2023 08:09:40 +0000
parents 58807b35777a
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32:628b235d76c7 33:f1738f8649b0
6 Preprocessing of FASTQ read files 6 Preprocessing of FASTQ read files
7 including trimming, quality filtering, cutadapt filtering and sampling 7 including trimming, quality filtering, cutadapt filtering and sampling
8 </description> 8 </description>
9 <requirements> 9 <requirements>
10 <requirement type="package">blast</requirement> 10 <requirement type="package">blast</requirement>
11 <requirement type="package">cutadapt</requirement> 11 <requirement type="package" version="4.4">cutadapt</requirement>
12 <requirement type="package">bioconductor-shortread</requirement> 12 <requirement type="package">bioconductor-shortread</requirement>
13 <requirement type="package">r-optparse</requirement> 13 <requirement type="package">r-optparse</requirement>
14 </requirements> 14 </requirements>
15 <required_files> 15 <required_files>
16 <include type="literal" path="single_fastq_filtering_wrapper.sh"/> 16 <include type="literal" path="single_fastq_filtering_wrapper.sh"/>
17 <include type="literal" path="single_fastq_filtering.R"/> 17 <include type="literal" path="single_fastq_filtering.R"/>
18 </required_files> 18 </required_files>
19 <command interpreter="bash"> 19 <command>
20 bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output} 20 bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output}
21 -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output} 21 -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output}
22 22
23 #if $sampling.sequence_sampling : 23 #if $sampling.sequence_sampling :
24 -n $sampling.sample_size 24 -n $sampling.sample_size