add test, test data, version, help

src/rseqc/rseqc_bamstat/config.vsh.yaml

@@ -20,31 +20,28 @@ argument_groups:
   - name: "--input"
     type: file 
     required: true
-    description: input alignment file in BAM or SAM format
-
+    description: Input alignment file in BAM or SAM format.
   - name: "--map_qual"
     type: integer
-    required: false
-    default: 30 
-    description: Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.
-    min: 0
+    example: 30 
+    description: |
+      Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: '30'.
     
 - name: "Output"
   arguments: 
   - name: "--output"
     type: file
     direction: output
-    required: false
-    default: $id.mapping_quality.txt
-    description: output file (txt) with mapping quality statistics
+    description: Output file (txt) with mapping quality statistics.
 
 resources:
   - type: bash_script
     path: script.sh
 test_resources:
   - type: bash_script
     path: test.sh
-  - path: /testData/unit_test_resources/sarscov2/test.paired_end.sorted.bam
+  - type: file
+    path: test_data
 
 engines:
 - type: docker
@@ -54,6 +51,9 @@ engines:
       packages: [ python3-pip ]
     - type: python
       packages: [ RSeQC ]
+    - type: docker
+      run: |
+        echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/software_versions.txt
 runners: 
 - type: executable
 - type: nextflow

src/rseqc/rseqc_bamstat/help.txt

@@ -0,0 +1,18 @@
+```
+bam_stat.py -h
+```
+
+Usage: bam_stat.py [options]
+
+Summarizing mapping statistics of a BAM or SAM file. 
+
+
+
+Options:
+  --version             show program's version number and exit
+  -h, --help            show this help message and exit
+  -i INPUT_FILE, --input-file=INPUT_FILE
+                        Alignment file in BAM or SAM format.
+  -q MAP_QUAL, --mapq=MAP_QUAL
+                        Minimum mapping quality (phred scaled) to determine
+                        "uniquely mapped" reads. default=30

src/rseqc/rseqc_bamstat/script.sh

@@ -1,8 +1,9 @@
 #!/bin/bash
 
+
 set -eo pipefail 
 
 bam_stat.py \
-    --input $par_input \
-    --mapq $par_map_qual \
+    --input "${par_input}" \
+    ${par_map_qual:+--mapq "${par_map_qual}"} \
 > $par_output

src/rseqc/rseqc_bamstat/test.sh

@@ -9,15 +9,41 @@ output_summary="mapping_quality.txt"
 echo "> Running $meta_functionality_name."
 
 "$meta_executable" \
-    --input "$meta_resources_dir/$input_bam" \
+    --input "$meta_resources_dir/test_data/$input_bam" \
     --output "$output_summary"
 
 exit_code=$?
 [[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
 
-echo ">> Checking whether output can be found and has content"
+echo ">> Checking whether output is present"
+[ ! -f "$output_summary" ] && echo "$output_summary file missing" && exit 1
+[ ! -s "$output_summary" ] && echo "$output_summary file is empty" && exit 1
+
+echo ">> Checking whether output is correct"
+diff "$meta_resources_dir/test_data/ref_output.txt" "$meta_resources_dir/$output_summary" || { echo "Output is not correct"; exit 1; }
+
+#############################################################################
 
+echo ">>> Test 2: Test with non-default mapping quality threshold"
+
+output_summary="mapping_quality_mapq_30.txt"
+
+# run executable and tests
+echo "> Running $meta_functionality_name."
+
+"$meta_executable" \
+    --input "$meta_resources_dir/test_data/$input_bam" \
+    --output "$output_summary" \
+    --map_qual 50
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Checking whether output is present"
 [ ! -f "$output_summary" ] && echo "$output_summary file missing" && exit 1
 [ ! -s "$output_summary" ] && echo "$output_summary file is empty" && exit 1
 
+echo ">> Checking whether output is correct"
+diff "$meta_resources_dir/test_data/ref_output_mapq.txt" "$meta_resources_dir/$output_summary" || { echo "Output is not correct"; exit 1; }
+
 exit 0

src/rseqc/rseqc_bamstat/test_data/ref_output.txt

@@ -0,0 +1,22 @@
+
+#==================================================
+#All numbers are READ count
+#==================================================
+
+Total records:                          200
+
+QC failed:                              0
+Optical/PCR duplicate:                  0
+Non primary hits                        0
+Unmapped reads:                         3
+mapq < mapq_cut (non-unique):           1
+
+mapq >= mapq_cut (unique):              196
+Read-1:                                 99
+Read-2:                                 97
+Reads map to '+':                       98
+Reads map to '-':                       98
+Non-splice reads:                       196
+Splice reads:                           0
+Reads mapped in proper pairs:           192
+Proper-paired reads map to different chrom:0

src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt

@@ -0,0 +1,22 @@
+
+#==================================================
+#All numbers are READ count
+#==================================================
+
+Total records:                          200
+
+QC failed:                              0
+Optical/PCR duplicate:                  0
+Non primary hits                        0
+Unmapped reads:                         3
+mapq < mapq_cut (non-unique):           20
+
+mapq >= mapq_cut (unique):              177
+Read-1:                                 88
+Read-2:                                 89
+Reads map to '+':                       96
+Reads map to '-':                       81
+Non-splice reads:                       177
+Splice reads:                           0
+Reads mapped in proper pairs:           175
+Proper-paired reads map to different chrom:0