Add CWLs for the tools used in disease-genome

Rename tool/curl to tool/wget

Imelement tool/wget

Add test for wget

Rename output object of wget from `output` to `downloaded`

Implement tool/tar

Minor fix for tar

Remove {tar,wget}.sh

Implement tool/cat

Implement tool/gunzip

Fix `doc` for gunzip

Implement tool/gzip

Implement tool/wc

Minor tweaks

test/data/sample.txt

@@ -0,0 +1 @@
+aaaa

test/tool/test_job/cat.yml

@@ -0,0 +1,3 @@
+files:
+  - class: File
+    location: ../../data/chr22.fa

test/tool/test_job/gunzip.yml

@@ -0,0 +1,3 @@
+file:
+  class: File
+  location: ../../data/test.tar.gz

test/tool/test_job/gzip.yml

@@ -0,0 +1,3 @@
+file:
+  class: File
+  location: ../../data/chr22.fa

test/tool/test_job/tar.yml

@@ -0,0 +1,6 @@
+file:
+  class: File
+  location: ../../data/test.tar.gz
+extract: true
+gzip: true
+verbose: true

test/tool/test_job/wc.yml

@@ -0,0 +1,3 @@
+file:
+  class: File
+  location: ../../data/sample.txt

test/tool/test_job/wget.yml

@@ -0,0 +1,3 @@
+use_remote_name: true  # type "boolean"
+url: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/master/README.md # type "string"
+track_location: false  # type "boolean"

tool/cat/cat.cwl

@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: concatenate files and print on the standard output
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+baseCommand: cat
+inputs:
+  files:
+    type: File[]
+    inputBinding: {}
+outputs:
+  concatinated: stdout
+  stderr: stderr
+stdout: cat-stdout.log
+stderr: cat-stderr.log

tool/cat/cat.yml

@@ -0,0 +1,3 @@
+files:  # array of type "File"
+  - class: File
+    path: a/file/path

tool/gunzip/gunzip.cwl

@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: decompression tool using Lempel-Ziv coding (LZ77)
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+baseCommand: [gunzip, --stdout]
+inputs:
+  file:
+    type: File
+    inputBinding: {}
+outputs:
+  decompressed: stdout
+  stderr: stderr
+stdout: $(inputs.file.nameroot)
+stderr: gunzip-stderr.log

tool/gunzip/gunzip.yml

@@ -0,0 +1,3 @@
+file:  # type "File"
+    class: File
+    path: a/file/path

tool/gzip/gzip.cwl

@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: compression/decompression tool using Lempel-Ziv coding (LZ77)
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+baseCommand: [gzip, -c]
+inputs:
+  file:
+    type: File
+    inputBinding: {}
+outputs:
+  compressed: stdout
+  stderr: stderr
+stdout: $(inputs.file.basename).gz
+stderr: gzip-stderr.log

tool/gzip/gzip.yml

@@ -0,0 +1,3 @@
+file:  # type "File"
+    class: File
+    path: a/file/path

tool/tar/tar.cwl

@@ -0,0 +1,43 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: manipulate tape archives
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+  InlineJavascriptRequirement: {}
+baseCommand: tar
+inputs:
+  file:
+    type: File
+    inputBinding:
+      prefix: --file=
+      separate: false
+  extract:
+    type: boolean
+    default: false
+    inputBinding:
+      prefix: -x
+  gzip:
+    type: boolean
+    default: false
+    inputBinding:
+      prefix: -z
+  verbose:
+    type: boolean
+    default: false
+    inputBinding:
+      prefix: -v
+outputs:
+  output:
+    type: Directory
+    outputBinding:
+      glob: |
+        ${
+          var extlen = inputs.gzip ? 2 : 1;
+          return inputs.file.basename.split('.').slice(0, -extlen).join('.');
+        }
+  stdout: stdout
+  stderr: stderr
+stdout: tar-stdout.log
+stderr: tar-stderr.log

tool/tar/tar.yml

@@ -0,0 +1,6 @@
+verbose: false  # type "boolean"
+gzip: false  # type "boolean"
+file:  # type "File"
+    class: File
+    path: a/file/path
+extract: false  # type "boolean"

tool/wc/wc.cwl

@@ -0,0 +1,35 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: print newline, word, and byte counts for each file
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+  InlineJavascriptRequirement: {}
+baseCommand: wc
+inputs:
+  file:
+    type: File
+    inputBinding: {}
+outputs:
+  lines:
+    type: int
+    outputBinding:
+      loadContents: true
+      glob: wc-stdout.txt
+      outputEval: $(Number(self[0].contents.trim().split(/\s+/)[0]))
+  words:
+    type: int
+    outputBinding:
+      loadContents: true
+      glob: wc-stdout.txt
+      outputEval: $(Number(self[0].contents.trim().split(/\s+/)[1]))
+  bytes:
+    type: int
+    outputBinding:
+      loadContents: true
+      glob: wc-stdout.txt
+      outputEval: $(Number(self[0].contents.trim().split(/\s+/)[2]))
+  stderr: stderr
+stdout: wc-stdout.txt
+stderr: wc-stderr.log

tool/wc/wc.yml

@@ -0,0 +1,3 @@
+file:  # type "File"
+    class: File
+    path: a/file/path

tool/wget/wget.cwl

@@ -0,0 +1,39 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: The non-interactive network downloader
+requirements:
+  DockerRequirement:
+    dockerPull: alpine:3.9
+  InlineJavascriptRequirement: {}
+baseCommand: wget
+inputs:
+  url:
+    doc: Download target URL
+    type: string
+    inputBinding: {}
+  output_name:
+    doc: Output file name (use `wget-stdout.txt` by default)
+    type: string
+    default: wget-stdout.txt
+    inputBinding:
+      prefix: --output-document=
+      separate: false
+      valueFrom: "$(inputs.use_remote_name ? inputs.url.split('/').pop() : self)"
+  use_remote_name:
+    doc: Use the basename of `url` parameter as an output file name. It is equivalent to `curl -O`.
+    type: boolean
+    default: false
+  track_location:
+    doc: Equivalent to `curl -L`
+    type: boolean
+    default: false
+    inputBinding:
+      prefix: --trusted-server-names
+outputs:
+  downloaded:
+    type: File
+    outputBinding:
+      glob: "$(inputs.use_remote_name ? inputs.url.split('/').pop() : inputs.output_name)"
+  stderr: stderr
+stderr: wget-stderr.log

tool/wget/wget.yml

@@ -0,0 +1,4 @@
+use_remote_name: false  # type "boolean"
+url: a_string  # type "string"
+track_location: false  # type "boolean"
+output_name: wget-stdout.txt  # default value of type "string".