diff --git a/src/gffread/config.vsh.yaml b/src/gffread/config.vsh.yaml index d2c41a87..7477a284 100644 --- a/src/gffread/config.vsh.yaml +++ b/src/gffread/config.vsh.yaml @@ -8,8 +8,6 @@ links: references: doi: 10.12688/f1000research.23297.2 license: MIT -requirements: - commands: [ gffread ] argument_groups: - name: Inputs arguments: @@ -52,7 +50,7 @@ argument_groups: required: true description: | Write the output records into . - default: output.gff + example: output.gff - name: --force_exons type: boolean_true description: | @@ -154,7 +152,6 @@ argument_groups: - name: --table type: string multiple: true - multiple_sep: "," description: | Output a simple tab delimited format instead of GFF, with columns having the values of GFF attributes given in ; special pseudo-attributes (prefixed by @) are diff --git a/src/gffread/script.sh b/src/gffread/script.sh index 9c4a2b8f..cd4abf14 100644 --- a/src/gffread/script.sh +++ b/src/gffread/script.sh @@ -50,6 +50,8 @@ [[ "$par_expose_dups" == "false" ]] && unset par_expose_dups [[ "$par_cluster_only" == "false" ]] && unset par_cluster_only +# if par_table is not empty, replace ";" with "," +par_table=$(echo "$par_table" | tr ';' ',') $(which gffread) \ "$par_input" \ diff --git a/src/gffread/test.sh b/src/gffread/test.sh index 326fce50..ea23edcb 100755 --- a/src/gffread/test.sh +++ b/src/gffread/test.sh @@ -86,7 +86,7 @@ diff "$expected_output_dir/transcripts.fa" "$test_output_dir/transcripts.fa" || echo "> Test 4 - Generate table from GFF annotation file" "$meta_executable" \ - --table @id,@chr,@start,@end,@strand,@exons,Name,gene,product \ + --table "@id;@chr;@start;@end;@strand;@exons;Name;gene;product" \ --outfile "$test_output_dir/annotation.tbl" \ --input "$test_dir/sequence.gff3" diff --git a/src/samtools/samtools_stats/config.vsh.yaml b/src/samtools/samtools_stats/config.vsh.yaml index 0d8f57a4..6daccf37 100644 --- a/src/samtools/samtools_stats/config.vsh.yaml +++ b/src/samtools/samtools_stats/config.vsh.yaml @@ -29,11 +29,10 @@ argument_groups: Reference file the CRAM was created with. - name: --coverage alternatives: -c - type: integer + type: string description: | - Coverage distribution min,max,step [1,1000,1]. - multiple: true - multiple_sep: ',' + Coverage distribution min;max;step. Default: `1;1000;1`. + example: '1;1000;1' - name: --remove_dups alternatives: -d type: boolean_true @@ -48,25 +47,25 @@ argument_groups: alternatives: -f type: string description: | - Required flag, 0 for unset. See also `samtools flags`. - default: "0" + Required flag, 0 for unset. See also `samtools flags`. Default: `"0"`. + example: "0" - name: --filtering_flag alternatives: -F type: string description: | - Filtering flag, 0 for unset. See also `samtools flags`. - default: "0" + Filtering flag, 0 for unset. See also `samtools flags`. Default: `0`. + example: "0" - name: --GC_depth type: double description: | - The size of GC-depth bins (decreasing bin size increases memory requirement). - default: 20000.0 + The size of GC-depth bins (decreasing bin size increases memory requirement). Default: `20000`. + example: 20000.0 - name: --insert_size alternatives: -i type: integer description: | - Maximum insert size. - default: 8000 + Maximum insert size. Default: `8000`. + example: 8000 - name: --id alternatives: -I type: string @@ -76,14 +75,14 @@ argument_groups: alternatives: -l type: integer description: | - Include in the statistics only reads with the given read length. - default: -1 + Include in the statistics only reads with the given read length. Default: `-1`. + example: -1 - name: --most_inserts alternatives: -m type: double description: | - Report only the main part of inserts. - default: 0.99 + Report only the main part of inserts. Default: `0.99`. + example: 0.99 - name: --split_prefix alternatives: -P type: string @@ -93,8 +92,8 @@ argument_groups: alternatives: -q type: integer description: | - The BWA trimming parameter. - default: 0 + The BWA trimming parameter. Default: `0`. + example: 0 - name: --ref_seq alternatives: -r type: file @@ -124,8 +123,8 @@ argument_groups: alternatives: -g type: integer description: | - Only bases with coverage above this value will be included in the target percentage computation. - default: 0 + Only bases with coverage above this value will be included in the target percentage computation. Default: `0`. + example: 0 - name: --input_fmt_option type: string description: | @@ -141,7 +140,7 @@ argument_groups: type: file description: | Output file. - default: "out.txt" + example: "out.txt" required: true direction: output diff --git a/src/samtools/samtools_stats/script.sh b/src/samtools/samtools_stats/script.sh index 6e32e9a5..e3872fc6 100644 --- a/src/samtools/samtools_stats/script.sh +++ b/src/samtools/samtools_stats/script.sh @@ -10,6 +10,9 @@ set -e [[ "$par_sparse" == "false" ]] && unset par_sparse [[ "$par_remove_overlaps" == "false" ]] && unset par_remove_overlaps +# change the coverage input from X;X;X to X,X,X +par_coverage=$(echo "$par_coverage" | tr ';' ',') + samtools stats \ ${par_coverage:+-c "$par_coverage"} \ ${par_remove_dups:+-d} \ diff --git a/src/samtools/samtools_stats/test.sh b/src/samtools/samtools_stats/test.sh index 05d70d30..b515100e 100644 --- a/src/samtools/samtools_stats/test.sh +++ b/src/samtools/samtools_stats/test.sh @@ -17,7 +17,7 @@ echo ">>> Checking whether output is non-empty" [ ! -s "$test_dir/test.paired_end.sorted.txt" ] && echo "File 'test.paired_end.sorted.txt' is empty!" && exit 1 echo ">>> Checking whether output is correct" -# compare using diff, ignoring the line stating the command that was passed. +# compare using diff, ignoring the line stating the command that was passed. diff <(grep -v "^# The command" "$test_dir/test.paired_end.sorted.txt") \ <(grep -v "^# The command" "$test_dir/ref.paired_end.sorted.txt") || \ (echo "Output file ref.paired_end.sorted.txt does not match expected output" && exit 1)