| Previous changeset 31:be1f407e1018 (2023-08-03) Next changeset 33:f1738f8649b0 (2023-08-04) |
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Commit message:
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty |
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modified:
RM_custom_search.py RM_custom_search.xml fasta_interlacer.xml fastq_name_affixer.xml paired_fastq_filtering_wrapper.sh sampleFasta.xml single_fastq_filtering_wrapper.sh summarize_cluster_table.xml |
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| diff -r be1f407e1018 -r 628b235d76c7 RM_custom_search.py --- a/RM_custom_search.py Thu Aug 03 10:54:34 2023 +0000 +++ b/RM_custom_search.py Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -57,10 +57,11 @@ def summarizeRepeatMaskerOutput(htmlout = "summary.html"): cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r" - args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table" ] + args = [ "Rscript", cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", + "RM-custom_output_table" ] status=subprocess.call(args) - cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" - args = [cmd, htmlout] + cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" + args = ["Rscript", cmd, htmlout] status=subprocess.call(args) return status |
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| diff -r be1f407e1018 -r 628b235d76c7 RM_custom_search.xml --- a/RM_custom_search.xml Thu Aug 03 10:54:34 2023 +0000 +++ b/RM_custom_search.xml Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -12,6 +12,8 @@ <required_files> <include type="literal" path="RM_custom_search.py"/> <include type="literal" path="parallel.py"/> + <include type="literal" path="rmsk_summary_table_multiple.r"/> + <include type="literal" path="RM_html_report.R"/> </required_files> |
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| diff -r be1f407e1018 -r 628b235d76c7 fasta_interlacer.xml --- a/fasta_interlacer.xml Thu Aug 03 10:54:34 2023 +0000 +++ b/fasta_interlacer.xml Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.4"> <description>Join pared reads into single file</description> <requirements> - <container type="package" version="3">python</container> + <requirement type="package" version="3">python</requirement> </requirements> <required_files> <include type="literal" path="fasta_interlacer.py"/> |
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| diff -r be1f407e1018 -r 628b235d76c7 fastq_name_affixer.xml --- a/fastq_name_affixer.xml Thu Aug 03 10:54:34 2023 +0000 +++ b/fastq_name_affixer.xml Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -7,7 +7,7 @@ <include type="literal" path="name_affixer.py"/> </required_files> <command> - ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n + python ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n $nspace > $output </command> |
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| diff -r be1f407e1018 -r 628b235d76c7 paired_fastq_filtering_wrapper.sh --- a/paired_fastq_filtering_wrapper.sh Thu Aug 03 10:54:34 2023 +0000 +++ b/paired_fastq_filtering_wrapper.sh Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -52,14 +52,14 @@ if [ -z "$CUTADAPT" ] # test if$CUTADAPT is empty then - ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + Rscript ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N $RENAME ${FILTER_SEQ[@]} else - ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + Rscript ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" $RENAME ${FILTER_SEQ[@]} fi -${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single +python ${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single rm $fasta_tmp_fileX |
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| diff -r be1f407e1018 -r 628b235d76c7 sampleFasta.xml --- a/sampleFasta.xml Thu Aug 03 10:54:34 2023 +0000 +++ b/sampleFasta.xml Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -2,6 +2,7 @@ <description> Tool for randomly sampling subsets of reads from large datasets</description> <requirements> <requirement type="package">seqkit</requirement> + <requirement type="package" version="3">python</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> |
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| diff -r be1f407e1018 -r 628b235d76c7 single_fastq_filtering_wrapper.sh --- a/single_fastq_filtering_wrapper.sh Thu Aug 03 10:54:34 2023 +0000 +++ b/single_fastq_filtering_wrapper.sh Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -47,10 +47,10 @@ if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty then - ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ + Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]} else - ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]} fi |
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| diff -r be1f407e1018 -r 628b235d76c7 summarize_cluster_table.xml --- a/summarize_cluster_table.xml Thu Aug 03 10:54:34 2023 +0000 +++ b/summarize_cluster_table.xml Fri Aug 04 07:37:49 2023 +0000 |
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| @@ -9,7 +9,7 @@ <required_files> <include type="literal" path="summarize_cluster_table.R"/> </required_files> - <command interpreter="Rscript" detect_errors="exit_code"> + <command detect_errors="exit_code"> Rscript $__tool_directory__/summarize_cluster_table.R --cluster_table=$cluster_table --output=$output |