Mercurial > repos > avowinkel > gatk
diff indel_realigner.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
| author | avowinkel |
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| date | Thu, 24 Sep 2015 12:10:01 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/indel_realigner.xml Thu Sep 24 12:10:01 2015 -0400 @@ -0,0 +1,90 @@ +<macros> + <xml name="IndelRealignerParameters" tokens="tag"> + + <expand macro="macro_bam_input" tag="@TAG@" /> + + <param name="targetIntervals" type="data" format="gatk_interval" label="Intervals file output from RealignerTargetCreator" help="-targetIntervals,--targetIntervals &lt;targetIntervals&gt;" /> + + <expand macro="macro_optional_parameters"> + <repeat name="knownAlleles" title="Input VCF file(s) with known indels" help="-known,‑‑knownAlleles &lt;knownAlleles&gt;"> + <param name="knownAllele" type="data" format="vcf" label="Variant file (VCF format)" /> + </repeat> + + <param name="consensusDeterminationModel" type="select" label="minimum reads at a locus to enable using the entropy calculation" help="-model,‑‑consensusDeterminationModel &lt;consensusDeterminationModel&gt;"> + <option value="USE_READS">USE_READS - Additionally uses indels already present in the original alignments of the reads</option> + <option value="KNOWNS_ONLY">KNOWNS_ONLYS - Uses only indels from a provided ROD of known indels</option> + <option value="USE_SW">USE_SW - Additionally uses 'Smith-Waterman' to generate alternate consenses</option> + </param> + <param name="LODThresholdForCleaning" type="float" value="5.0" label="LOD threshold above which the cleaner will clean" help="-LOD,‑‑LODThresholdForCleaning &lt;LODThresholdForCleaning&gt;" /> + <!--param name="nWayOut" type="float" value="5.0" label="Generate one output file for each input (-I) bam file (not compatible with -output)" help="-nWayOut,--nWayOut &lt;nWayOut&gt;" /--> + </expand> + + + <expand macro="macro_advanced_parameters"> + <param name="entropyThreshold" type="float" value="0.15" label="Percentage of mismatches at a locus to be considered having high entropy (0.0 < entropy <= 1.0)" help="-entropy,‑‑entropyThreshold &lt;entropyThreshold&gt;" /> + + <param name="maxConsensuses" type="integer" value="30" label="Max alternate consensuses to try (necessary to improve performance in deep coverage)" help="-maxConsensuses,‑‑maxConsensuses &lt;maxConsensuses&gt;" /> + + <param name="maxIsizeForMovement" type="integer" value="3000" label="maximum insert size of read pairs that we attempt to realign" help="-maxIsize,‑‑maxIsizeForMovement &lt;maxIsizeForMovement&gt;" /> + + <param name="maxPositionalMoveAllowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,‑‑maxPositionalMoveAllowed &lt;maxPositionalMoveAllowed&gt;" /> + + <param name="maxReadsForConsensuses" type="integer" value="120" label="Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)" help="-greedy,‑‑maxReadsForConsensuses &lt;maxReadsForConsensuses&gt;" /> + + <param name="maxReadsForRealignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,‑‑maxReadsForRealignment &lt;maxReadsForRealignment&gt;" /> + + <param name="maxReadsInMemory" type="integer" value="150000" label="max reads allowed to be kept in memory at a time by the SAMFileWriter" help="-maxInMemory,‑‑maxReadsInMemory &lt;maxReadsInMemory&gt;" /> + + <param name="noOriginalAlignmentTags" type="boolean" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,‑‑noOriginalAlignmentTags" /> + </expand> + + </xml> + + <xml name="IndelRealignerOutput"> + <data format="bam" name="ir_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)"> + <yield /> + </data> + </xml> + + <template name="IndelRealignerPreprocessing"> +<![CDATA[ + @token_bam_input_pre@ + + ln -s -f ${analysis_type.targetIntervals} target.intervals && + + #if $analysis_type.optional_parameters.optional_parameters_enabled + #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles): + ln -s -f ${knownAllele.knownAllele} knownAllele_${i}.vcf && + #end for + #end if +]]> + </template> + + <template name="IndelRealignerOptions"> +<![CDATA[ + --out ${ir_output_bam} + + @token_bam_input@ + --targetIntervals target.intervals + + #if $analysis_type.optional_parameters.optional_parameters_enabled + #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles): + --knownAlleles knownAllele_${i}.vcf + #end for + --consensusDeterminationModel ${analysis_type.consensusDeterminationModel} + --LODThresholdForCleaning ${analysis_type.LODThresholdForCleaning} + #end if + + #if $analysis_type.advanced_parameters.advanced_parameters_enabled + --entropyThreshold ${analysis_type.advanced_parameters.entropyThreshold} + --maxConsensuses ${analysis_type.advanced_parameters.maxConsensuses} + --maxIsizeForMovement ${analysis_type.advanced_parameters.maxIsizeForMovement} + --maxPositionalMoveAllowed ${analysis_type.advanced_parameters.maxPositionalMoveAllowed} + --maxReadsForConsensuses ${analysis_type.advanced_parameters.maxReadsForConsensuses} + --maxReadsForRealignment ${analysis_type.advanced_parameters.maxReadsForRealignment} + --maxReadsInMemory ${analysis_type.advanced_parameters.maxReadsInMemory} + ${analysis_type.advanced_parameters.noOriginalAlignmentTags} + #end if +]]> + </template> +</macros>