| Previous changeset 32:628b235d76c7 (2023-08-04) Next changeset 34:91996b991991 (2024-02-16) |
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Commit message:
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty |
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modified:
paired_fastq_filtering.R paired_fastq_filtering.xml single_fastq_filtering.R single_fastq_filtering.xml |
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| diff -r 628b235d76c7 -r f1738f8649b0 paired_fastq_filtering.R --- a/paired_fastq_filtering.R Fri Aug 04 07:37:49 2023 +0000 +++ b/paired_fastq_filtering.R Fri Aug 04 08:09:40 2023 +0000 |
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| @@ -182,7 +182,7 @@ cutadapt_cmd = function(input, output, cutadapt_arguments) { - cmds = paste("cutadapt --format=", "fastq", cutadapt_arguments, " ", c(input), + cmds = paste("cutadapt ", cutadapt_arguments, " ", c(input), " -o ", c(output), sep = "") } |
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| diff -r 628b235d76c7 -r f1738f8649b0 paired_fastq_filtering.xml --- a/paired_fastq_filtering.xml Fri Aug 04 07:37:49 2023 +0000 +++ b/paired_fastq_filtering.xml Fri Aug 04 08:09:40 2023 +0000 |
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| @@ -9,7 +9,7 @@ </description> <requirements> <requirement type="package">blast</requirement> - <requirement type="package">cutadapt</requirement> + <requirement type="package" version="4.4">cutadapt</requirement> <requirement type="package">bioconductor-shortread</requirement> <requirement type="package">r-optparse</requirement> </requirements> @@ -19,6 +19,7 @@ <include type="literal" path="fasta_interlacer.py"/> </required_files> <command> + cutadapt --version; bash '$__tool_directory__'/paired_fastq_filtering_wrapper.sh -a ${A} -b ${B} -o ${paired} -c ${cut_off} -p ${percent_above} -N ${max_n} $rename -G ${png_output} |
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| diff -r 628b235d76c7 -r f1738f8649b0 single_fastq_filtering.R --- a/single_fastq_filtering.R Fri Aug 04 07:37:49 2023 +0000 +++ b/single_fastq_filtering.R Fri Aug 04 08:09:40 2023 +0000 |
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| @@ -143,8 +143,7 @@ cutadapt_cmd=function(input,output,cutadapt_arguments){ - cmds=paste("cutadapt --format=", - "fastq", + cmds=paste("cutadapt ", cutadapt_arguments, " ", c(input), |
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| diff -r 628b235d76c7 -r f1738f8649b0 single_fastq_filtering.xml --- a/single_fastq_filtering.xml Fri Aug 04 07:37:49 2023 +0000 +++ b/single_fastq_filtering.xml Fri Aug 04 08:09:40 2023 +0000 |
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| @@ -8,7 +8,7 @@ </description> <requirements> <requirement type="package">blast</requirement> - <requirement type="package">cutadapt</requirement> + <requirement type="package" version="4.4">cutadapt</requirement> <requirement type="package">bioconductor-shortread</requirement> <requirement type="package">r-optparse</requirement> </requirements> @@ -16,7 +16,7 @@ <include type="literal" path="single_fastq_filtering_wrapper.sh"/> <include type="literal" path="single_fastq_filtering.R"/> </required_files> - <command interpreter="bash"> + <command> bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output} -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output} |