Required Changes

src/bedtools/bedtools_bamtofastq/config.vsh.yaml

@@ -1,13 +1,14 @@
 name: bedtools_bamtofastq
 namespace: bedtools
-description: Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
+description: | 
+  Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
 keywords: [Conversion ,BAM, FASTQ]
 links:
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
   repository: https://github.com/arq5x/bedtools2
 references:
   doi: 10.1093/bioinformatics/btq033
-license: GPL-2.0, MIT
+license: MIT
 requirements:
   commands: [bedtools]
 authors:
@@ -25,19 +26,19 @@ argument_groups:
 
   - name: Outputs
     arguments:
-      - name: --output_fq
+      - name: --fastq
         alternatives: -fq
         direction: output
         type: file
         description: Output FASTQ file.
         required: true
 
-      - name: --output_fq2
+      - name: --fastq2
         alternatives: -fq2
         type: file
         direction: output
         description: |
-          FASTQ for second end.  Used if BAM contains paired-end data.
+          FASTQ for second end. Used if BAM contains paired-end data.
           BAM should be sorted by query name is creating paired FASTQ.
          
   - name: Options

src/bedtools/bedtools_bamtofastq/script.sh

@@ -9,8 +9,8 @@
 # Execute bedtools bamtofastq with the provided arguments
 bedtools bamtofastq \
     ${par_tags:+-tags} \
-    ${par_output_fq2:+-fq2 "$par_output_fq2"} \
+    ${par_fastq2:+-fq2 "$par_fastq2"} \
     -i "$par_input" \
-    -fq "$par_output_fq"
+    -fq "$par_fastq"
 
 

src/bedtools/bedtools_bamtofastq/test.sh

@@ -29,7 +29,7 @@ cd test1
 echo "> Run bedtools bamtofastq on BAM file"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output.fastq"
+  --fastq "output.fastq"
 
 # checks
 assert_file_exists "output.fastq"
@@ -46,7 +46,7 @@ cd test2
 echo "> Run bedtools bamtofastq on BAM file with tags"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output.fastq" \
+  --fastq "output.fastq" \
   --tags
 
 # checks
@@ -64,8 +64,8 @@ cd test3
 echo "> Run bedtools bamtofastq on BAM file with output_fq2"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output1.fastq" \
-  --output_fq2 "output2.fastq" 
+  --fastq "output1.fastq" \
+  --fastq2 "output2.fastq" 
 
 # checks
 assert_file_exists "output1.fastq"