add collect-columns

collect-columns.wdl

+version 1.0
+
+task CollectColumns {
+    input {
+        Array[File]+ inputTables
+        String outputPath
+        Int? featureColumn
+        Int? valueColumn
+        Int? separator
+        Array[String]? sampleNames
+        Boolean header = false
+        Array[String]? additionalAttributes
+        File? referenceGtf
+        String featureAttribute
+
+        String dockerTag = "0.1.1--py_0"
+    }
+
+    command {
+        collect-columns \
+        ~{outputPath} \
+        ~{sep=" " inputTables} \
+        ~{"-f "  + featureColumn} \
+        ~{"-c " + valueColumn} \
+        ~{"-s " + separator} \
+        ~{true="-n" false="" defined(sampleNames)} ~{sep=" " sampleNames} \
+        ~{true="-H" false="" header} \
+        ~{true="-a" false="" defined(additionalAttributes)} ~{sep=" " additionalAttributes} \
+        ~{"-g " + referenceGtf} \
+        ~{"-F " + featureAttribute}
+    }
+
+    output {
+        File outputTable = outputPath
+    }
+
+    runtime {
+        memory: 4 + ceil(0.5* length(inputTables))
+        docker: "quay.io/biocontainers/collect-columns:" + dockerTag
+    }
+}
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