Gunzip

CHANGELOG.md

@@ -1,5 +1,9 @@
 # toolbox v0.1.1
 
+## NEW FEATURES
+`gunzip`: Add gunzip functionality to decompress gzip-compressed files.
+
+
 ## MINOR CHANGES
 
 * Updated the test CI (PR #6).

src/gunzip/config.vsh.yaml

@@ -0,0 +1,96 @@
+name: gunzip
+description: Decompress files compressed with gzip
+keywords: [ "decompress", "gzip", "gunzip", "*.gz" ]
+links:
+  homepage: https://www.gnu.org/software/gzip/manual/
+  documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+  repository: https://cgit.git.savannah.gnu.org/cgit/gzip.git/
+  issue_tracker: https://savannah.gnu.org/bugs/?group=gzip          # Tracker turned off by group.
+license: GPL-3.0
+requirements:
+  commands: [ gunzip ]
+
+argument_groups:
+- name: Inputs
+  arguments:
+  - name: --input
+    type: file 
+    direction: input
+    description: Path of file to be decompressed
+    required: true
+
+- name: Outputs
+  arguments:  
+  - name: --output
+    type: file
+    direction: output
+    required: true
+    description: Decompressed file 
+
+- name: Arguments
+  arguments:
+  - name: --force
+    alternatives: -f
+    type: boolean_true
+    description: force overwrite of output file and compress links
+  - name: --keep
+    alternatives: -k
+    type: boolean_true
+    description: keep input files
+  - name: --list 
+    alternatives: -l
+    type: boolean_true
+    description: list compressed file contents
+  - name: --no_name
+    alternatives: -n
+    type: boolean_true
+    description: do not save or restore the original name and time stamp
+  - name: --name
+    alternatives: -N
+    type: boolean_true
+    description: save or restore the original name and time stamp
+  - name: --quiet
+    alternatives: -q
+    type: boolean_true
+    description: suppress all warnings
+  - name: --recursive
+    alternatives: -r
+    type: boolean_true
+    description: operate recursively on directories
+  - name: --suffix
+    alternatives: -S
+    type: string
+    description: Uncompress all files in the current working directory whose suffix matches a given pattern
+  - name: --synchronous
+    type: boolean_true
+    description: synchronous output (safer if system crashes, but slower)
+  - name: --test
+    alternatives: -t
+    type: boolean_true
+    description: test compressed file integrity
+  - name: --verbose
+    alternatives: -v
+    type: boolean_true
+    description: verbose mode
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+
+engines:
+  - type: docker
+    image: quay.io/biocontainers/gzip:1.11
+    setup:
+      - type: docker
+        run: |
+          gunzip --version | sed 's/gunzip, version\s\(.*\)/gunzip: "\1"/' > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow

src/gunzip/help.txt

@@ -0,0 +1,7 @@
+cat <<EOF > src/gunzip/help.txt
+```sh
+gunzip --help
+```
+EOF
+
+docker run quay.io/biocontainers/gzip:1.11 gunzip --help >> src/gunzip/help.txt

src/gunzip/script.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+[[ "$par_force" == "false" ]] && unset par_force
+[[ "$par_keep" == "false" ]] && unset par_keep
+[[ "$par_list" == "false" ]] && unset par_list
+[[ "$par_no_name" == "false" ]] && unset par_no_name
+[[ "$par_name" == "false" ]] && unset par_name
+[[ "$par_quiet" == "false" ]] && unset par_quiet
+[[ "$par_recursive" == "false" ]] && unset par_recursive
+[[ "$par_suffix" == "false" ]] && unset par_suffix
+[[ "$par_synchronous" == "false" ]] && unset par_synchronous
+[[ "$par_test" == "false" ]] && unset par_test
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+gunzip -c \
+    ${par_force:+-f } \
+    ${par_keep:+-k } \
+    ${par_list:+-l } \
+    ${par_no_name:+-n } \
+    ${par_name:+-N } \
+    ${par_quiet:+-q } \
+    ${par_recursive:+-r } \
+    ${par_suffix:+-S "${par_suffix}"} \
+    ${par_synchronous: } \
+    ${par_test:+-t } \
+    ${par_verbose:+-v } \
+    "$par_input" > "$par_output"

src/gunzip/test.sh

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+set -e
+
+## VIASH START
+## VIASH END
+
+"$meta_executable" --input "$meta_resources_dir/test_data/test.vcf.gz" --output "test.vcf"
+
+echo ">> Checking output of decompressing"
+[ ! -f "test.vcf" ] && echo "Output file test.vcf does not exist" && exit 1
+
+echo "> Test successful"

src/gunzip/test_data/script.sh

@@ -0,0 +1,13 @@
+# bgzip test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/bgzip/test.
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/bgzip/test/test.vcf src/gunzip/test_data/test.vcf
+
+gzip src/gunzip/test_data/test.vcf
+
+rm -rf /tmp/snakemake-wrappers