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comparison indel_realigner.xml @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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-1:000000000000 0:b80ff7f43ad1
1 <macros>
2 <xml name="IndelRealignerParameters" tokens="tag">
3
4 <expand macro="macro_bam_input" tag="@TAG@" />
5
6 <param name="targetIntervals" type="data" format="gatk_interval" label="Intervals file output from RealignerTargetCreator" help="-targetIntervals,--targetIntervals &amp;lt;targetIntervals&amp;gt;" />
7
8 <expand macro="macro_optional_parameters">
9 <repeat name="knownAlleles" title="Input VCF file(s) with known indels" help="-known,&#8209;&#8209;knownAlleles &amp;lt;knownAlleles&amp;gt;">
10 <param name="knownAllele" type="data" format="vcf" label="Variant file (VCF format)" />
11 </repeat>
12
13 <param name="consensusDeterminationModel" type="select" label="minimum reads at a locus to enable using the entropy calculation" help="-model,&#8209;&#8209;consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
14 <option value="USE_READS">USE_READS - Additionally uses indels already present in the original alignments of the reads</option>
15 <option value="KNOWNS_ONLY">KNOWNS_ONLYS - Uses only indels from a provided ROD of known indels</option>
16 <option value="USE_SW">USE_SW - Additionally uses 'Smith-Waterman' to generate alternate consenses</option>
17 </param>
18 <param name="LODThresholdForCleaning" type="float" value="5.0" label="LOD threshold above which the cleaner will clean" help="-LOD,&#8209;&#8209;LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
19 <!--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,&#45;&#45;nWayOut &amp;lt;nWayOut&amp;gt;" /-->
20 </expand>
21
22
23 <expand macro="macro_advanced_parameters">
24 <param name="entropyThreshold" type="float" value="0.15" label="Percentage of mismatches at a locus to be considered having high entropy (0.0 &lt; entropy &lt;= 1.0)" help="-entropy,&#8209;&#8209;entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
25
26 <param name="maxConsensuses" type="integer" value="30" label="Max alternate consensuses to try (necessary to improve performance in deep coverage)" help="-maxConsensuses,&#8209;&#8209;maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
27
28 <param name="maxIsizeForMovement" type="integer" value="3000" label="maximum insert size of read pairs that we attempt to realign" help="-maxIsize,&#8209;&#8209;maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
29
30 <param name="maxPositionalMoveAllowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,&#8209;&#8209;maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
31
32 <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,&#8209;&#8209;maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
33
34 <param name="maxReadsForRealignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,&#8209;&#8209;maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
35
36 <param name="maxReadsInMemory" type="integer" value="150000" label="max reads allowed to be kept in memory at a time by the SAMFileWriter" help="-maxInMemory,&#8209;&#8209;maxReadsInMemory &amp;lt;maxReadsInMemory&amp;gt;" />
37
38 <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,&#8209;&#8209;noOriginalAlignmentTags" />
39 </expand>
40
41 </xml>
42
43 <xml name="IndelRealignerOutput">
44 <data format="bam" name="ir_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)">
45 <yield />
46 </data>
47 </xml>
48
49 <template name="IndelRealignerPreprocessing">
50 <![CDATA[
51 @token_bam_input_pre@
52
53 ln -s -f ${analysis_type.targetIntervals} target.intervals &&
54
55 #if $analysis_type.optional_parameters.optional_parameters_enabled
56 #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles):
57 ln -s -f ${knownAllele.knownAllele} knownAllele_${i}.vcf &&
58 #end for
59 #end if
60 ]]>
61 </template>
62
63 <template name="IndelRealignerOptions">
64 <![CDATA[
65 --out ${ir_output_bam}
66
67 @token_bam_input@
68 --targetIntervals target.intervals
69
70 #if $analysis_type.optional_parameters.optional_parameters_enabled
71 #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles):
72 --knownAlleles knownAllele_${i}.vcf
73 #end for
74 --consensusDeterminationModel ${analysis_type.consensusDeterminationModel}
75 --LODThresholdForCleaning ${analysis_type.LODThresholdForCleaning}
76 #end if
77
78 #if $analysis_type.advanced_parameters.advanced_parameters_enabled
79 --entropyThreshold ${analysis_type.advanced_parameters.entropyThreshold}
80 --maxConsensuses ${analysis_type.advanced_parameters.maxConsensuses}
81 --maxIsizeForMovement ${analysis_type.advanced_parameters.maxIsizeForMovement}
82 --maxPositionalMoveAllowed ${analysis_type.advanced_parameters.maxPositionalMoveAllowed}
83 --maxReadsForConsensuses ${analysis_type.advanced_parameters.maxReadsForConsensuses}
84 --maxReadsForRealignment ${analysis_type.advanced_parameters.maxReadsForRealignment}
85 --maxReadsInMemory ${analysis_type.advanced_parameters.maxReadsInMemory}
86 ${analysis_type.advanced_parameters.noOriginalAlignmentTags}
87 #end if
88 ]]>
89 </template>
90 </macros>