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annotate base_recalibrator.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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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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1 <macros>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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2 <xml name="BaseRecalibratorParameters" tokens="tag">
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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4 <expand macro="macro_bam_input" tag="@TAG@" />
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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6 <param name="knownSites" type="data" format="vcf,bcf,bed,pileup,tabular,table" label="Database of known Sites (ROD files; e.g. VCF format)" multiple="true" title="A database of known polymorphic sites to skip over in the recalibration algorithm" help="-knownSites,&#8209;&#8209;knownSites &amp;lt;knownSites&amp;gt;" />
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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8 </xml>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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10 <xml name="BaseRecalibratorOutput">
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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11 <data format="tabular" name="br_table" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (Table)">
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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12 <yield />
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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13 </data>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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14 </xml>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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16 <template name="BaseRecalibratorPreprocessing">
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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17 <![CDATA[
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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18 @token_bam_input_pre@
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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19 #for $i, $variant in enumerate($analysis_type.knownSites):
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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20 ln -s -f ${variant} variant_${i}.vcf &&
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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21 #end for
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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22 ]]>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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23 </template>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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25 <template name="BaseRecalibratorOptions">
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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26 <![CDATA[
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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27 --out ${br_table}
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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29 @token_bam_input@
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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31 #for $i, $variant in enumerate($analysis_type.knownSites):
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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32 --knownSites variant_${i}.vcf
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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33 #end for
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34 ]]>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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35 </template>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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36 </macros>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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