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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
author iuc
date Tue, 05 Aug 2025 13:47:58 +0000
parents 85dc96ebc770
children
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.10</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
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6 <requirement type="package" version="1.22">samtools</requirement>
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7 <requirement type="package" version="9.5">coreutils</requirement>
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8 <yield />
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9 </requirements>
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10 </xml>
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11 <xml name="version_command">
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12 <version_command>freebayes --version | cut -d v -f 3</version_command>
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13 </xml>
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14 <xml name="citations">
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15 <citations>
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16 <citation type="bibtex">
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17 @misc{1207.3907,
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18 Author = {Erik Garrison},
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19 Title = {Haplotype-based variant detection from short-read sequencing},
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20 Year = {2012},
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21 Eprint = {arXiv:1207.3907},
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22 url = {http://arxiv.org/abs/1207.3907}
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23 }
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24 </citation>
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25 <yield />
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26 </citations>
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27 </xml>
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28 <xml name="validation">
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29 <validator type="unspecified_build" />
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30 <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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31 </xml>
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32 <xml name="input_bam">
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33 <conditional name="batchmode">
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34 <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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35 <option value="individual" selected="true">Run individually</option>
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36 <option value="merge">Merge output VCFs</option>
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37 </param>
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38 <when value="individual">
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39 <param name="input_bams" type="data" format="bam,cram" label="BAM or CRAM dataset">
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40 <yield />
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41 </param>
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42 </when>
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43 <when value="merge">
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44 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="BAM or CRAM dataset(s)">
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45 <yield />
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46 </param>
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47 </when>
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48 </conditional>
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49 </xml>
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50 <token name="@COVERAGE@">
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51 --min-coverage ${coverage_options.min_coverage}
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52 --skip-coverage ${coverage_options.skip_coverage}
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53 --limit-coverage ${coverage_options.limit_coverage}
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54 </token>
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55 <xml name="par_min_cov">
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56 <param argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
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57 <param argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
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58 <param argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
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59 </xml>
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60 </macros>