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1 <macros>
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2 <token name="@DEPENDENCY_VERSION@">1.3.1</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
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6 <requirement type="package" version="1.9">samtools</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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10 <xml name="citations">
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11 <citations>
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12 <citation type="bibtex">
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13 @misc{1207.3907,
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14 Author = {Erik Garrison},
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15 Title = {Haplotype-based variant detection from short-read sequencing},
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16 Year = {2012},
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17 Eprint = {arXiv:1207.3907},
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18 url = {http://arxiv.org/abs/1207.3907}
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19 }
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20 </citation>
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21 <yield />
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22 </citations>
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23 </xml>
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24 <xml name="validation">
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25 <validator type="unspecified_build" />
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26 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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27 </xml>
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28 <xml name="input_bam">
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29 <conditional name="batchmode">
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30 <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio">
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31 <option value="individual" selected="true">Run individually</option>
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32 <option value="merge">Merge output VCFs</option>
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33 </param>
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34 <when value="individual">
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35 <param name="input_bams" type="data" format="bam" label="BAM dataset">
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36 <yield />
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37 </param>
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38 </when>
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39 <when value="merge">
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40 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)">
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41 <yield />
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42 </param>
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43 </when>
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44 </conditional>
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45 </xml>
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46 <token name="@COVERAGE@">
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47 --min-coverage ${options_type.min_coverage}
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48 --skip-coverage ${options_type.skip_coverage}
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49 --limit-coverage ${options_type.limit_coverage}
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50 </token>
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51 <xml name="par_min_cov">
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52 <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
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53 <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
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54 <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
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55 </xml>
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56 </macros>
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