diff --git a/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java b/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java index bf88a964595..520e32d764a 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/CreateBundle.java @@ -22,7 +22,7 @@ /** *
* Create a single bundle (JSON) file for one or more related inputs, for use as input to a GATK tool. - *
An example bundle JSON file is show below. The bundle has 3 resources, with content types + *
+ * An example bundle JSON file is show below. The bundle has 3 resources, with content types * "HAPLOID_REFERENCE", "REFERENCE_DICTIONARY", and "REFERENCE_INDEX" respectively, with the "HAPLOID_REFERENCE" * resource designated as the primary resource. This bundle is a reference bundle, and can be used as an * input where ever a reference argument is required. @@ -51,7 +51,7 @@ * "primary": "HAPLOID_REFERENCE" * } * - *
* CreateBundle requires at least one primary resource input. One or more optional secondary resource inputs * may also be supplied. @@ -79,7 +79,7 @@ *
* Bundle output file names must end with the suffix ".json". *
- *
- *
* 1) Create a resource bundle for a VCF from just the VCF, letting the tool resolve the secondary (index) resource by * automatically finding the sibling index file, and letting the tool determine the content types. If the sibling index @@ -150,7 +150,7 @@ * --secondary:CT_VARIANTS_INDEX some/other/path/to/vcd.idx \ * --output mybundle.json *
- *
* 1) Create a resource bundle for a reference from just the .fasta, letting the tool resolve the secondary * (index and dictionary) resource by automatically finding the sibling files, and determining the content types. @@ -179,7 +179,7 @@ * --secondary:CT_HAPLOID_REFERENCE_INDEX some/other/path/to/my.fai \ * --secondary:CT_HAPLOID_REFERENCE_DICTIONARY some/other/path/to/my.dict \ * --output mybundle.json - *
+ * * 4) Create a resource bundle for a fasta, but specify the fasta, index and dictionary resources and the content * types explicitly. The resulting bundle will contain the fasta, index and dictionary resources: *
@@ -188,7 +188,7 @@ * --secondary:CT_HAPLOID_REFERENCE_INDEX some/other/path/to/my.fai \ * --secondary:CT_HAPLOID_REFERENCE_DICTIONARY some/other/path/to/my.dict \ * --output mybundle.json - *
+ * */ @DocumentedFeature @CommandLineProgramProperties(