/tools/gatk/realigner_target_creator.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 165 lines · 145 code · 20 blank · 0 comment · 0 complexity · 0daf04f37014a978b8dd20549cd01e47 MD5 · raw file
- <tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
- <description>for use in local realignment</description>
- <requirements>
- <requirement type="package" version="1.3">gatk</requirement>
- <requirement type="package">samtools</requirement>
- </requirements>
- <macros>
- <import>gatk_macros.xml</import>
- </macros>
- <command interpreter="python">gatk_wrapper.py
- --max_jvm_heap_fraction "1"
- --stdout "${output_log}"
- -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
- #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
- -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
- #end if
- -p 'java
- -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
- -T "RealignerTargetCreator"
- -o "${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}"
- #end if
- '
- #set $rod_binding_names = dict()
- #for $rod_binding in $rod_bind:
- #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
- #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
- #else
- #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
- #end if
- #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
- -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
- #end for
-
- #include source=$standard_gatk_options#
- ##start analysis specific options
- #if $analysis_param_type.analysis_param_type_selector == "advanced":
- -p '
- --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"
- --windowSize "${analysis_param_type.windowSize}"
- --mismatchFraction "${analysis_param_type.mismatchFraction}"
- --maxIntervalSize "${analysis_param_type.maxIntervalSize}"
- '
- #end if
- </command>
- <inputs>
- <conditional name="reference_source">
- <expand macro="reference_source_selector_param" />
- <when value="cached">
- <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;">
- <validator type="unspecified_build" />
- <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" help="-R,--reference_sequence &lt;reference_sequence&gt;" >
- <options from_data_table="gatk_picard_indexes">
- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
- </options>
- <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
- </param>
- </when>
- <when value="history">
- <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" />
- <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;">
- <options>
- <filter type="data_meta" key="dbkey" ref="input_bam" />
- </options>
- </param>
- </when>
- </conditional>
-
- <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &lt;known&gt;">
- <conditional name="rod_bind_type">
- <param name="rod_bind_type_selector" type="select" label="Binding Type">
- <option value="dbsnp" selected="True">dbSNP</option>
- <option value="snps">SNPs</option>
- <option value="indels">INDELs</option>
- <option value="custom">Custom</option>
- </param>
- <when value="dbsnp">
- <param name="input_rod" type="data" format="vcf" label="ROD file" />
- </when>
- <when value="snps">
- <param name="input_rod" type="data" format="vcf" label="ROD file" />
- </when>
- <when value="indels">
- <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" label="ROD file" />
- </when>
- </conditional>
- </repeat>
-
- <expand macro="gatk_param_type_conditional" />
-
- <expand macro="analysis_type_conditional">
- <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &lt;windowSize&gt;" />
- <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction &lt;mismatchFraction&gt;)"/>
- <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &lt;minReadsAtLocus&gt;" />
- <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &lt;maxIntervalSize&gt;" />
- </expand>
- </inputs>
- <outputs>
- <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
- <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
- </outputs>
- <tests>
- <test>
- <param name="reference_source_selector" value="history" />
- <param name="ref_file" value="phiX.fasta" ftype="fasta" />
- <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
- <param name="rod_bind_type_selector" value="dbsnp" />
- <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
- <param name="gatk_param_type_selector" value="basic" />
- <param name="analysis_param_type_selector" value="advanced" />
- <param name="windowSize" value="10" />
- <param name="mismatchFraction" value="0.15" />
- <param name="minReadsAtLocus" value="4" />
- <param name="maxIntervalSize" value="500" />
- <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
- <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
- </test>
- </tests>
- <help>
- **What it does**
- Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
- For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_.
- To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
- If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
- ------
- **Inputs**
- GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.
- **Outputs**
- The output is in GATK Interval format.
- Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
- -------
- **Settings**::
- windowSize window size for calculating entropy or SNP clusters
- mismatchFraction fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1
- minReadsAtLocus minimum reads at a locus to enable using the entropy calculation
- maxIntervalSize maximum interval size
- @CITATION_SECTION@
- </help>
- </tool>