1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/34fffbf01183/ changeset: 34fffbf01183 user: dan date: 2011-10-25 21:43:04 summary: Add metadata validator to force input bam files to have bam_index metadata files for GATK tools. affected #: 6 files diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -138,6 +138,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -147,7 +148,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -107,6 +107,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -116,7 +117,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -103,6 +103,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -112,7 +113,9 @@ </param></when><when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -117,6 +117,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -126,7 +127,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -135,6 +135,7 @@ <repeat name="input_bams" title="Sample BAM file" min="1"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat> @@ -146,7 +147,9 @@ </when><when value="history"><!-- FIX ME!!!! --><repeat name="input_bams" title="Sample BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param></repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -145,6 +145,7 @@ <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /><param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -156,7 +157,9 @@ <when value="history"><!-- FIX ME!!!! --><param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" /> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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