diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml index 1c871cc9..7e9742c8 100644 --- a/v1.0/conformance_test_v1.0.yaml +++ b/v1.0/conformance_test_v1.0.yaml @@ -1593,3 +1593,25 @@ inputs are not present in the input object used to run the tool. should_fail: true tags: [ required ] + +- tool: v1.0/awk-awk.cwl + job: v1.0/awk-awk-job.yaml + doc: test that a $ in the baseCommand is not interpreted by the shell + output: + bRegionsNonZero: + basename: awk-awk-input_nonZero.txt + class: File + checksum: "sha1$810037850eb6f1791e9365e25f124808828070e2" + size: 24 + tags: [ required ] + +- tool: v1.0/awk-awk2.cwl + job: v1.0/awk-awk-job.yaml + doc: test that a $ in an argument is not interpreted by the shell + output: + bRegionsNonZero: + basename: awk-awk-input_nonZero.txt + class: File + checksum: "sha1$810037850eb6f1791e9365e25f124808828070e2" + size: 24 + tags: [ required ] diff --git a/v1.0/v1.0/awk-awk-input b/v1.0/v1.0/awk-awk-input new file mode 100644 index 00000000..7c16ebf2 --- /dev/null +++ b/v1.0/v1.0/awk-awk-input @@ -0,0 +1,2 @@ +this will be ignored 0 +this will be selected 1 diff --git a/v1.0/v1.0/awk-awk-job.yaml b/v1.0/v1.0/awk-awk-job.yaml new file mode 100644 index 00000000..c1fdd51d --- /dev/null +++ b/v1.0/v1.0/awk-awk-job.yaml @@ -0,0 +1,3 @@ +atoBComparison: + class: File + path: awk-awk-input diff --git a/v1.0/v1.0/awk-awk.cwl b/v1.0/v1.0/awk-awk.cwl new file mode 100644 index 00000000..860a8b20 --- /dev/null +++ b/v1.0/v1.0/awk-awk.cwl @@ -0,0 +1,13 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: CommandLineTool +inputs: + atoBComparison: + type: File + inputBinding: + position: 1 +outputs: + bRegionsNonZero: + type: stdout +stdout: $(inputs.atoBComparison.basename)_nonZero.txt +baseCommand: [awk, "$5!=0"] diff --git a/v1.0/v1.0/awk-awk2.cwl b/v1.0/v1.0/awk-awk2.cwl new file mode 100644 index 00000000..06660b11 --- /dev/null +++ b/v1.0/v1.0/awk-awk2.cwl @@ -0,0 +1,14 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: CommandLineTool +inputs: + atoBComparison: + type: File + inputBinding: + position: 1 +outputs: + bRegionsNonZero: + type: stdout +stdout: $(inputs.atoBComparison.basename)_nonZero.txt +baseCommand: awk +arguments: ["$5!=0"]