From db0b97b3cb7d13f4c3dfad37b808dc9467c95987 Mon Sep 17 00:00:00 2001 From: Nirmayi Date: Tue, 30 Jan 2024 18:06:05 +0100 Subject: [PATCH] Use full argument names in descriptions --- src/featurecounts/config.vsh.yaml | 18 +++++++++--------- src/featurecounts/script.sh | 3 +-- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/src/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml index f7fa1a04..993266a4 100644 --- a/src/featurecounts/config.vsh.yaml +++ b/src/featurecounts/config.vsh.yaml @@ -20,16 +20,16 @@ functionality: alternatives: ["-a"] type: file description: | - Name of an annotation file. GTF/GFF format by default. See -F option for more format information. + Name of an annotation file. GTF/GFF format by default. See '--format' option for more format information. required: true example: annotation.gtf - name: --input alternatives: ["-i"] type: file multiple: true - multiple_sep: ',' + multiple_sep: ';' description: | - A comma-separated list of SAM or BAM format files. They can be either name or location sorted. Location-sorted paired-end reads are automatically sorted by read names. + A list of SAM or BAM format files separated by semi-colon (;). They can be either name or location sorted. Location-sorted paired-end reads are automatically sorted by read names. required: true example: input_file1.bam @@ -54,7 +54,7 @@ functionality: type: file direction: output description: | - Count of number of reads supporting each exon-exon junction. See -J for more information. + Count of number of reads supporting each exon-exon junction. See '--junctions' for more information. must_exist: false example: features.txt.jcounts must_exist: false @@ -118,7 +118,7 @@ functionality: alternatives: ["-O"] type: boolean_true description: | - Assign reads to all their overlapping meta-features (or features if -f is specified). + Assign reads to all their overlapping meta-features (or features if '--feature_level' is specified). - name: --min_overlap type: integer description: | @@ -185,7 +185,7 @@ functionality: - name: --fraction type: boolean_true description: | - Assign fractional counts to features. This option must be used together with '-M' or '-O' or both. When '-M' is specified, each reported alignment from a multi-mapping read (identified via 'NH' tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When '-O' is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both '-M' and '-O' are specified, each alignment will carry a fractional count of 1/(x*y). + Assign fractional counts to features. This option must be used together with '--multi_mapping' or '--overlapping' or both. When '--multi_mapping' is specified, each reported alignment from a multi-mapping read (identified via 'NH' tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When '--overlapping' is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both '--multi_mapping' and '--overlapping' are specified, each alignment will carry a fractional count of 1/(x*y). - name: Read filtering arguments: @@ -235,7 +235,7 @@ functionality: alternatives: ["-G"] type: file description: | - Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files. This optional argument can be used with '-J' option to improve read counting for junctions. + Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files. This optional argument can be used with '--junctions' option to improve read counting for junctions. required: false example: reference.fasta @@ -259,7 +259,7 @@ functionality: alternatives: ["-P"] type: boolean_true description: | - Check validity of paired-end distance when counting read pairs. Use -d and -D to set thresholds. + Check validity of paired-end distance when counting read pairs. Use '--min_length' and '--max_length' to set thresholds. - name: --min_length alternatives: ["-d"] type: integer @@ -313,7 +313,7 @@ functionality: - name: --tmpdir type: file description: | - Directory under which intermediate files are saved (later removed). By default, intermediate files will be saved to the directory specified in '-o' argument. + Directory under which intermediate files are saved (later removed). By default, intermediate files will be saved to the directory specified in the '--output' argument. required: false - name: --max_M_op type: integer diff --git a/src/featurecounts/script.sh b/src/featurecounts/script.sh index f55e400f..b0efb2c5 100644 --- a/src/featurecounts/script.sh +++ b/src/featurecounts/script.sh @@ -32,7 +32,7 @@ fi [[ "$par_verbose" == "false" ]] && unset par_verbose [[ "$par_version" == "false" ]] && unset par_version -IFS="," read -ra input <<< $par_input +IFS=";" read -ra input <<< $par_input featureCounts \ ${par_format:+-F "${par_format}"} \ @@ -76,7 +76,6 @@ featureCounts \ ${par_tmpdir:+--tmpDir "${par_tmpdir}"} \ ${par_max_M_op:+--maxMOp "${par_max_M_op}"} \ ${par_verbose:+--verbose} \ - ${par_version:+-v} \ ${meta_cpus:+-T "${meta_cpus}"} \ -a "$par_annotation" \ -o "$par_output" \