Remove multiple_sep (#78)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586b.

* get rid of multiple_sep fields in configs

* Fix coverage argument's format in config

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 <outfile>.
-        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 <attrlist>; special pseudo-attributes (prefixed by @) are 

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" \

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"
 

src/samtools/samtools_stats/config.vsh.yaml

@@ -30,10 +30,10 @@ argument_groups:
     - name: --coverage
       alternatives: -c
       type: integer
-      description: |
-        Coverage distribution min,max,step [1,1000,1].
       multiple: true
-      multiple_sep: ','
+      description: |
+        Coverage distribution min;max;step. Default: [1, 1000, 1].
+      example: [1, 1000, 1]
     - name: --remove_dups
       alternatives: -d
       type: boolean_true
@@ -48,25 +48,25 @@ 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 +76,14 @@ 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 +93,8 @@ 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 +124,8 @@ 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 +141,7 @@ argument_groups:
       type: file
       description: |
         Output file.
-      default: "out.txt"
+      example: "out.txt"
       required: true
       direction: output
 

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} \

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)