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GATK tools will now use gatk_picard_indexes data table.

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This commit is contained in:
Daniel Blankenberg
2011-10-31 09:41:09 -04:00
parent 2a3d2894dd
commit 74c5e42ecd
15 changed files with 29 additions and 19 deletions
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tool_data_table_conf.xml.sample
+5
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@@ -70,6 +70,11 @@
<columns>value, dbkey, name, path</columns>
<file path="tool-data/picard_index.loc" />
</table>
<!-- Location of Picard dict files valid for GATK -->
<table name="gatk_picard_indexes" comment_char="#">
<columns>value, dbkey, name, path, tools_valid_for</columns>
<file path="tool-data/picard_index.loc" />
</table>
<!-- Location of SRMA dict file and other files -->
<table name="srma_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
tools/gatk/analyze_covariates.xml
+1
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@@ -11,6 +11,7 @@
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar"
-recalFile "${input_recal}"
-outputDir "${output_html.files_path}"
##--num_threads 4 ##hard coded, for now
##-log "${output_log}"
##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
-resources "${GALAXY_DATA_INDEX_DIR}/gatk/R"
tools/gatk/count_covariates.xml
+2 -2
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@@ -139,10 +139,10 @@
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
</options>
</param>
tools/gatk/indel_realigner.xml
+3 -2
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@@ -13,6 +13,7 @@
-T "IndelRealigner"
-o "${output_bam}"
-et "NO_ET" ##ET no phone home
##--num_threads 4 ##hard coded, for now
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
-R "${reference_source.ref_file.fields.path}"
@@ -108,10 +109,10 @@
<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 -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_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">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
</options>
</param>
tools/gatk/realigner_target_creator.xml
+3 -2
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@@ -13,6 +13,7 @@
-T "RealignerTargetCreator"
-o "${output_interval}"
-et "NO_ET" ##ET no phone home
##--num_threads 4 ##hard coded, for now
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
-R "${reference_source.ref_file.fields.path}"
@@ -104,10 +105,10 @@
<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 -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_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">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
</options>
</param>
tools/gatk/table_recalibration.xml
+3 -2
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@@ -13,6 +13,7 @@
-T "TableRecalibration"
-o "${output_bam}"
-et "NO_ET" ##ET no phone home
##--num_threads 4 ##hard coded, for now
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
-R "${reference_source.ref_file.fields.path}"
@@ -118,10 +119,10 @@
<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 -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_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">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
</options>
</param>
tools/gatk/unified_genotyper.xml
+2 -2
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@@ -136,11 +136,11 @@
<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 -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_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>
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
</options>
</param>
tools/gatk/variant_annotator.xml
+2 -2
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@@ -146,10 +146,10 @@
<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 -->
<validator type="dataset_metadata_in_data_table" table_name="gatk_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">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
</options>
</param>
tools/gatk/variant_apply_recalibration.xml
+1 -1
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@@ -102,7 +102,7 @@
<param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
<param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
</options>
</param>
tools/gatk/variant_combine.xml
+1 -1
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@@ -114,7 +114,7 @@
</param>
</repeat>
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
</options>
</param>
tools/gatk/variant_eval.xml
+1 -1
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@@ -159,7 +159,7 @@
<param name="input_variant" type="data" format="vcf" label="Input variant file" />
</repeat>
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
</options>
</param>
tools/gatk/variant_filtration.xml
+1 -1
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@@ -106,7 +106,7 @@
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
</options>
</param>
tools/gatk/variant_recalibrator.xml
+1 -1
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@@ -152,7 +152,7 @@
<param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
</repeat>
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
</options>
</param>
tools/gatk/variants_validate.xml
+2 -1
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@@ -12,6 +12,7 @@
-T "ValidateVariants"
-et "NO_ET" ##ET no phone home
--num_threads 4 ##hard coded, for now
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
-R "${reference_source.ref_file.fields.path}"
@@ -91,7 +92,7 @@
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Input variant file" />
<param name="ref_file" type="select" label="Using reference genome">
<options from_data_table="picard_indexes">
<options from_data_table="gatk_picard_indexes">
<filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
</options>
</param>
tools/picard/picard_ReorderSam.xml
+1 -1
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@@ -4,7 +4,7 @@
picard_wrapper.py
--input=$inputFile
#if $source.indexSource == "built-in"
--ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }"
--ref="${source.ref.fields.path}"
#else
--ref-file=$refFile
--species-name=$source.speciesName