annotate realigner_target_creator.xml @ 0:b80ff7f43ad1 draft default tip

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 <macros>
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2 <xml name="RealignerTargetCreatorParameters" tokens="tag">
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4 <expand macro="macro_bam_input" tag="@TAG@" />
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6 <expand macro="macro_optional_parameters">
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7 <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,&#8209;&#8209;maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
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8 <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,&#8209;&#8209;minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
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9 <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,&#8209;&#8209;windowSize &amp;lt;windowSize&amp;gt;" />
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11 <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,&#8209;&#8209;mismatchFraction &amp;lt;mismatchFraction&amp;gt;" />
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12 <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,&#8209;&#8209;known &amp;lt;known&amp;gt;">
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13 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
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14 </repeat>
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15 </expand>
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17 </xml>
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19 <xml name="RealignerTargetCreatorOutput">
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20 <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)">
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21 <yield />
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22 </data>
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23 </xml>
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25 <template name="RealignerTargetCreatorPreprocessing">
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26 <![CDATA[
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27 @token_bam_input_pre@
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29 #if $analysis_type.optional_parameters.optional_parameters_enabled
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30 #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
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31 ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf &&
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32 #end for
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33 #end if
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34 ]]>
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35 </template>
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37 <template name="RealignerTargetCreatorOptions">
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38 <![CDATA[
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39 --out ${rtc_output_intervals}
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41 @token_bam_input@
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43 #if $analysis_type.optional_parameters.optional_parameters_enabled
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44 --maxIntervalSize ${analysis_type.optional_parameters.maxIntervalSize}
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45 --minReadsAtLocus ${analysis_type.optional_parameters.minReadsAtLocus}
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46 --windowSize ${analysis_type.optional_parameters.windowSize}
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47 --mismatchFraction ${analysis_type.optional_parameters.mismatchFraction}
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49 #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
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50 --known rod_binding_${i}.vcf
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51 #end for
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52 #end if
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53 ]]>
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54 </template>
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55 </macros>
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