1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/945c7a47755f/ changeset: 945c7a47755f user: dan date: 2011-11-21 22:41:19 summary: Remove no longer supported ROD datatypes from GATK tools (version 1.3). affected #: 2 files

diff -r 88afa15e556dfea22d34b0a78ffc3ebe162b64f7 -r 945c7a47755f4c468d0742ad02d43647a300565c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -147,17 +147,17 @@ <option value="custom">Custom</option></param><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when></conditional></repeat>

diff -r 88afa15e556dfea22d34b0a78ffc3ebe162b64f7 -r 945c7a47755f4c468d0742ad02d43647a300565c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -179,7 +179,7 @@ <option value="custom">Custom</option></param><when value="variant"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" /> + <param name="input_rod" type="data" format="vcf" label="Variant ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -198,7 +198,7 @@ </conditional></when><when value="comp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> @@ -218,7 +218,7 @@ </conditional></when><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -237,7 +237,7 @@ </conditional></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -256,7 +256,7 @@ </conditional></when><when value="hapmap"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -275,7 +275,7 @@ </conditional></when><when value="omni"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -294,7 +294,7 @@ </conditional></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -314,7 +314,7 @@ </when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>

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