Update unix tool property names

PMCC-BioinformaticsCore · Jul 10, 2019 · c578197 · c578197
1 parent d0494e7
commit c578197
Show file tree

Hide file tree

Showing 8 changed files with 21 additions and 208 deletions.
diff --git a/tools/cat.py b/tools/cat.py
@@ -1,3 +1,5 @@
+from janis import ToolOutput, Stdout
+
 from janis.tool.commandtool import ToolInput
 from janis.types.common_data_types import Array, File
 from janis.unix.tools.unixtool import UnixTool
@@ -19,7 +21,7 @@ def inputs(self):
         return [ToolInput("files", Array(File()))]
 
     def outputs(self):
-        return []
+        return [ToolOutput("out", Stdout())]
 
     @staticmethod
     def docker():

diff --git a/tools/compile.py b/tools/compile.py
@@ -13,13 +13,13 @@ class Compile(UnixTool):
     def tool():
         return "javaCompiler"
 
+    def friendly_name(self):
+        return "Java compiler"
+
     @staticmethod
     def base_command():
         return "javac"
 
-    def friendly_name(self):
-        return "Java compiler"
-
     @staticmethod
     def docker():
         return "openjdk:8"
@@ -31,4 +31,4 @@ def inputs(self):
         return [ToolInput("file", File(), position=1)]
 
     def outputs(self):
-        return [ToolOutput("compiled", File(), glob=WildcardSelector("*.class"))]
+        return [ToolOutput("out", File(), glob=WildcardSelector("*.class"))]
diff --git a/tools/echo.py b/tools/echo.py
@@ -5,7 +5,7 @@
 class Echo(UnixTool):
     @staticmethod
     def tool():
-        return "Echo"
+        return "echo"
 
     def friendly_name(self):
         return "Echo - Print to console"
@@ -19,7 +19,3 @@ def inputs(self):
 
     def outputs(self):
         return [ToolOutput("out", Stdout())]
-
-    @staticmethod
-    def docker():
-        return "ubuntu:latest"
diff --git a/tools/merge.py b/tools/merge.py
@@ -18,8 +18,4 @@ def inputs(self):
         return [ToolInput("files", Array(File()))]
 
     def outputs(self):
-        return [ToolOutput("merged", Stdout())]
-
-    @staticmethod
-    def docker():
-        return "ubuntu:latest"
+        return [ToolOutput("out", Stdout())]
diff --git a/tools/scatterlines.py b/tools/scatterlines.py
diff --git a/tools/tar.py b/tools/tar.py
@@ -1,7 +1,7 @@
 #
 # Untar a file
-
 from janis import Array, ToolInput, ToolOutput, InputSelector, File, Filename
+from janis.unix.data_types.tarfile import TarFile
 from janis.unix.tools.unixtool import UnixTool
 
 
@@ -21,96 +21,12 @@ def inputs(self):
         return [
             ToolInput("files", Array(File()), position=2),
             ToolInput("files2", Array(File(), optional=True), position=3),
-            ToolInput("tarName", Filename(extension=".tar"), position=1),
+            ToolInput("outputFilename", Filename(extension=".tar"), position=1),
         ]
 
     def outputs(self):
-        return [ToolOutput("tarred", File(), glob=InputSelector("tarName"))]
-
-    @staticmethod
-    def docker():
-        return "ubuntu:latest"
+        return [ToolOutput("out", TarFile(), glob=InputSelector("outputFilename"))]
 
 
 if __name__ == "__main__":
     print(Tar().help())
-
-"""
-
-EXAMPLE XML
-
-        <Step>
-            <title>Tar</title>
-            <author>Michael Franklin</author>
-            <cores>1</cores>
-            <ram>1024</ram>
-            <label>{{label}}</label>
-            <supportedTypes>
-                <type>cwl</type>
-                <type>wdl</type>
-            </supportedTypes>
-        
-            <inputs>
-                <input>
-                    <tag>input2</tag>
-                    <type>File</type>
-                </input>
-                <input>
-                    <tag>input2</tag>
-                    <type>File</type>
-                </input>
-            </inputs>
-            <outputs>
-                <output>
-                    <tag>output</tag>
-                    <type>File</type>
-                </output>
-            </outputs>
-        </Step>
-
-==============================
-
-        class: CommandLineTool
-        cwlVersion: v1.0
-        id: tar
-        baseCommand:
-          - tar
-          - cvf
-        inputs:
-          - id: tarName
-            type: string?
-            inputBinding:
-              position: 0
-          - id: input1
-            type:
-              - File
-            inputBinding:
-              position: 1
-          - id: input2
-            type:
-              - File
-            inputBinding:
-              position: 2
-        outputs:
-          - id: output
-            type: File?
-            outputBinding:
-              glob: '*'
-        label: tar
-
-  ========================================
-  
-        task SingleTar {
-            String tarName
-            File input1
-            File input2
-        
-            command {
-                tar cvf ${tarName} ${input1} ${input2}
-            }
-        
-            output {
-                File out = glob("*")[0]
-            }
-        }
-"""
diff --git a/tools/unixtool.py b/tools/unixtool.py
@@ -7,3 +7,7 @@ class UnixTool(CommandTool, ABC):
     @staticmethod
     def tool_module():
         return "unix"
+
+    @staticmethod
+    def docker():
+        return "ubuntu:latest"
diff --git a/tools/untar.py b/tools/untar.py
@@ -5,87 +5,18 @@
 
 class Untar(UnixTool):
     @staticmethod
-    def base_command():
-        return ["tar", "xf"]
+    def tool():
+        return "untar"
 
     def friendly_name(self):
         return "Untar archive"
 
     @staticmethod
-    def tool():
-        return "Untar"
+    def base_command():
+        return ["tar", "xf"]
 
     def inputs(self):
         return [ToolInput("tarFile", TarFile(), position=0)]
 
     def outputs(self):
-        return [ToolOutput("files", Array(File()), glob=WildcardSelector("*.java"))]
-
-    @staticmethod
-    def docker():
-        return "ubuntu:latest"
-
-
-"""
-
-EXAMPLE XML
-
-<Step>
-    <title>Untar</title>
-    <author>Michael Franklin</author>
-    <cores>1</cores>
-    <ram>1024</ram>
-    <label>{{label}}</label>
-    <supportedTypes>
-        <type>cwl</type>
-        <type>wdl</type>
-    </supportedTypes>
-    
-    <inputs>
-        <input>
-            <tag>input</tag>
-            <type>File</type>
-        </input>
-    </inputs>
-    <outputs>
-        <output>
-            <tag>output</tag>
-            <type>File</type>
-        </output>
-    </outputs>
-</Step>
-
-+ provide CWL template
-
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: [tar, xf]
-inputs:
-  input:
-    type: File
-    inputBinding:
-      position: 1
-  output:
-    type: string
-    inputBinding:
-      position: 2
-
-outputs:
-  example_out:
-    type: File
-    outputBinding:
-      glob: $(inputs.outputfile)
-
-+ wdl template
-
-task {
-    File input
-    File output
-    command {
-        tar -xf ${input}
-    }
-}
-
-"""
+        return [ToolOutput("out", Array(File()), glob=WildcardSelector("*.java"))]