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annotate bamtools.xml @ 5:befc9dad4ca8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author iuc
date Sat, 27 Nov 2021 10:02:03 +0000
parents 4d343c1f606b
children e4490b16f0d7
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76b2f1eee508 Uploaded
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1 <?xml version="1.0"?>
5
befc9dad4ca8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
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2 <tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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3 <description>BAM datasets and perform other transformations</description>
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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4 <macros>
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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5 <import>macros.xml</import>
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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6 </macros>
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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7 <expand macro="requirements" />
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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8 <command detect_errors="exit_code">
3
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9 <![CDATA[
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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10 ##set up input files
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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11 ln -s '${input_bams}' localbam.bam &&
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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12 ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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13 #if str( $analysis_type.analysis_type_selector ) == 'convert':
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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14 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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15 #set $reference_fasta_filename = 'localref.fa'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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16 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == 'history':
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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17 ln -s '${analysis_type.format_type.reference_source.ref_file}' '${reference_fasta_filename}' &&
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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18 samtools faidx '${reference_fasta_filename}' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 &&
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19 #else:
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20 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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21 #end if
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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22 #end if
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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23 #end if
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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24 bamtools
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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25 #if str( $analysis_type.analysis_type_selector ) == 'convert':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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26 convert
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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27 -format ${analysis_type.format_type.format_type_selector}
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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28 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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29 ${analysis_type.format_type.mapqual}
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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30 -fasta '${reference_fasta_filename}'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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31 #elif str( $analysis_type.format_type.format_type_selector ) == 'sam':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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32 ${analysis_type.format_type.noheader}
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33 #end if
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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34 -out '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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35 #elif str( $analysis_type.analysis_type_selector ) == 'count':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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36 count
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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37 > '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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38 #elif str( $analysis_type.analysis_type_selector ) == 'coverage':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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39 coverage
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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40 -out '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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41 #elif str( $analysis_type.analysis_type_selector ) == 'header':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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42 header
4
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43 > '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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44 #elif str( $analysis_type.analysis_type_selector ) == 'merge':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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45 merge
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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46 -out '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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47 #elif str( $analysis_type.analysis_type_selector ) == 'random':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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48 random
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49 -n ${analysis_type.count}
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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50 -seed ${analysis_type.seed}
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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51 -out '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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52 #elif str( $analysis_type.analysis_type_selector ) == 'revert':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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53 revert
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54 ${analysis_type.keepDuplicate}
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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55 ${analysis_type.keepQualities}
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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56 -out '$out_file1'
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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57 #elif str( $analysis_type.analysis_type_selector ) == 'sort':
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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58 sort
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59 ${analysis_type.byname}
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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60 -out '$out_file1'
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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61 #end if
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4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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62 -in localbam.bam
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63 ]]>
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64 </command>
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65 <inputs>
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66 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
3
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67 <conditional name="analysis_type">
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68 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
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69 <option value="convert">Convert</option>
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70 <option value="count">Count</option>
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71 <option value="coverage">Coverage</option>
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72 <option value="header">Header</option>
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73 <option value="merge">Merge</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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74 <option value="random">Random</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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75 <option value="revert">Revert</option>
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76 <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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77 <!-- Allowing users for sort files may break donstream functionality. -->
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78 <!-- To enable sort option simply uncomment the line below: -->
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79 <!-- <option value="sort">Sort</option> -->
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80 </param>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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81 <when value="convert">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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82 <conditional name="format_type">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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83 <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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84 <option value="bed">BED</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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85 <option value="fasta">FASTA</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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86 <option value="fastq">FASTQ</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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87 <option value="json">JSON</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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88 <option value="pileup">Pileup</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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89 <option value="sam">SAM</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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90 <option value="yaml">YAML</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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91 </param>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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92 <when value="bed"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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93 <when value="fasta"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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94 <when value="fastq"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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95 <when value="json"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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96 <when value="yaml"/>
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97 <when value="pileup">
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98 <conditional name="reference_source">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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99 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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100 <option value="cached">Locally cached</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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101 <option value="history">History</option>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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102 </param>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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103 <when value="cached">
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104 <param name="ref_file" type="select" label="Using reference genome">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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105 <options from_data_table="sam_fa_indexes">
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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106 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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107 </options>
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108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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109 </param>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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110 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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111 <when value="history"> <!-- FIX ME!!!! -->
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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112 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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113 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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114 </conditional>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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115 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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116 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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117 <when value="sam">
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118 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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119 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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120 </conditional>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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121 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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122 <when value="count" />
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123 <when value="coverage" />
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124 <when value="header" />
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125 <when value="merge" />
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126 <when value="random">
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127 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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128 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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129 </when>
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130 <when value="revert">
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131 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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132 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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133 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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134 <!--
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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135 <when value="sort">
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136 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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137 </when>
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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138 -->
0
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139 </conditional>
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140 </inputs>
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141 <outputs>
3
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142 <data format="txt" name="out_file1">
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143 <change_format>
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144 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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145 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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146 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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147 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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148 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
4
4d343c1f606b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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149 <when input="analysis_type.analysis_type_selector" value="count" format="tabular" />
3
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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150 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
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151 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
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152 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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153 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
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154 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
04866f817daa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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155 </change_format>
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156 </data>
0
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157 </outputs>
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158 <tests>
3
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159 <test>
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160 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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161 <param name="analysis_type_selector" value="convert"/>
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162 <param name="format_type_selector" value="pileup"/>
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163 <param name="reference_source_selector" value="history" />
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164 <param name="mapqual" value="true" />
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165 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
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166 <output name="out_file1" file="bamtools-convert-pileup.pu" />
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167 </test>
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168 <test>
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169 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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170 <param name="analysis_type_selector" value="count"/>
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171 <output name="out_file1" file="bamtools-count.tab" />
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172 </test>
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173 <test>
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174 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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175 <param name="analysis_type_selector" value="coverage"/>
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176 <output name="out_file1" file="bamtools-coverage.tab" />
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177 </test>
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178 <test>
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179 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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180 <param name="analysis_type_selector" value="header"/>
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181 <output name="out_file1" file="bamtools-header.txt" />
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182 </test>
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183 </tests>
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184 <help>
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185
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186 **What is does**
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187
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188 BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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189 This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.
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190
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191 -----
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192
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193 **Convert**
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194
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195 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
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196 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
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197
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198 -----
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199
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200 **Count**
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201
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202 Counts a number of alignments in a BAM dataset(s).
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203
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204 -----
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205
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206 **Coverage**
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207
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208 Prints per-base coverage for a BAM dataset.
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209
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210 -----
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211
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212 **Header**
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213
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214 Prints header from a BAM dataset(s).
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215
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216 ------
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217
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218 **Merge**
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219
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220 Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.
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221
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222 ------
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223
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224 **Random**
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225
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226 Grabs a specified number of random lines from BAM dataset(s).
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227
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228 ------
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229
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230 **Revert**
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231
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232 Removes duplicate marks and restores original (non-recalibrated) base qualities.
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233
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234 -----
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235
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236 .. class:: infomark
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237
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238 **More information**
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239
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240 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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241
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242 </help>
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243 <citations>
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244 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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245 </citations>
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246 </tool>