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annotate bamtools.xml @ 2:524f8dfc3c84 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author devteam
date Wed, 18 Jan 2017 11:46:46 -0500
parents 0d2ddd67b743
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1 <?xml version="1.0"?>
2
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2 <tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0">
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3 <description>BAM datasets and perform other transformations</description>
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4 <requirements>
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5 <requirement type="package" version="2.4.0">bamtools</requirement>
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6 <requirement type="package" version="1.3.1">samtools</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command>
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12 <![CDATA[
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13 ##set up input files
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14 #for $bam_count, $input_bam in enumerate( $input_bams ):
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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15 ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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16 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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17 #end for
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18 #if str( $analysis_type.analysis_type_selector ) == "convert":
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19 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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20 #set $reference_fasta_filename = "localref.fa"
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21 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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22 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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23 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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24 #else:
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25 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
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26 #end if
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27 #end if
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28 #end if
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29 bamtools
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30 #if str( $analysis_type.analysis_type_selector ) == "convert":
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31 convert
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32 -format ${analysis_type.format_type.format_type_selector}
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33 #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
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34 ${analysis_type.format_type.mapqual}
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35 -fasta "${reference_fasta_filename}"
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36 #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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37 ${analysis_type.format_type.noheader}
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38 #end if
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39 -out $out_file1
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40 #elif str( $analysis_type.analysis_type_selector ) == "count":
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41 count
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42 > $out_file1
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43 #elif str( $analysis_type.analysis_type_selector ) == "coverage":
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44 coverage
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45 -out $out_file1
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46 #elif str( $analysis_type.analysis_type_selector ) == "header":
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47 header
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48 > $out_file1
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49 #elif str( $analysis_type.analysis_type_selector ) == "merge":
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50 merge
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51 -out $out_file1
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52 #elif str( $analysis_type.analysis_type_selector ) == "random":
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53 random
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54 -n ${analysis_type.count}
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55 -seed ${analysis_type.seed}
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56 -out $out_file1
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57 #elif str( $analysis_type.analysis_type_selector ) == "revert":
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58 revert
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59 ${analysis_type.keepDuplicate}
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60 ${analysis_type.keepQualities}
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61 -out $out_file1
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62 #elif str( $analysis_type.analysis_type_selector ) == "sort":
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63 sort
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64 ${analysis_type.byname}
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65 -out $out_file1
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66 #end if
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67 #for $bam_count, $input_bam in enumerate( $input_bams ):
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68 -in "localbam_${bam_count}.bam"
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69 #end for
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70 ]]>
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71 </command>
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72 <inputs>
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73 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
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74 <conditional name="analysis_type">
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75 <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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76 <option value="convert">Convert</option>
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77 <option value="count">Count</option>
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78 <option value="coverage">Coverage</option>
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79 <option value="header">Header</option>
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80 <option value="merge">Merge</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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81 <option value="random">Random</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents: 1
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82 <option value="revert">Revert</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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83 <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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84 <!-- Allowing users for sort files may break donstream functionality. -->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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85 <!-- To enable sort option simply uncomment the line below: -->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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86 <!-- <option value="sort">Sort</option> -->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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87 </param>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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88 <when value="convert">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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89 <conditional name="format_type">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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90 <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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91 <option value="bed">BED</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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92 <option value="fasta">FASTA</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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93 <option value="fastq">FASTQ</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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94 <option value="json">JSON</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents: 1
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95 <option value="pileup">Pileup</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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96 <option value="sam">SAM</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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97 <option value="yaml">YAML</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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98 </param>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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99 <when value="bed"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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parents: 1
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100 <when value="fasta"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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101 <when value="fastq"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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102 <when value="json"/>
524f8dfc3c84 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="yaml"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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104 <when value="pileup">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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105 <conditional name="reference_source">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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106 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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107 <option value="cached">Locally cached</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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108 <option value="history">History</option>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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109 </param>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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110 <when value="cached">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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diff changeset
111 <param name="ref_file" type="select" label="Using reference genome">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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112 <options from_data_table="sam_fa_indexes">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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113 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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114 </options>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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115 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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116 </param>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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117 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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118 <when value="history"> <!-- FIX ME!!!! -->
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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119 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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120 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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121 </conditional>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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122 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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123 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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124 <when value="sam">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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125 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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126 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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127 </conditional>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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128 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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129 <when value="count" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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130 <when value="coverage" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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131 <when value="header" />
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132 <when value="merge" />
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133 <when value="random">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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134 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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135 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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136 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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137 <when value="revert">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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138 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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139 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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140 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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141 <!--
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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142 <when value="sort">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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143 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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144 </when>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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145 -->
0
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146 </conditional>
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147 </inputs>
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148 <outputs>
2
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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149 <data format="txt" name="out_file1">
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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150 <change_format>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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151 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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152 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
524f8dfc3c84 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.format_type.format_type_selector" value="fastq" format="fastq" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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154 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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155 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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156 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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157 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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158 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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159 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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160 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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161 </change_format>
524f8dfc3c84 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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162 </data>
0
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163 </outputs>
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164 <tests>
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165 <test>
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166 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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167 <param name="analysis_type_selector" value="convert"/>
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168 <param name="format_type_selector" value="pileup"/>
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169 <param name="reference_source_selector" value="history" />
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170 <param name="mapqual" value="true" />
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171 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
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172 <output name="output_bam" file="bamtools-convert-pileup.pu" />
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173 </test>
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174 <test>
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175 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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176 <param name="analysis_type_selector" value="count"/>
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177 <output name="output_bam" file="bamtools-count.tab" />
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178 </test>
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179 <test>
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180 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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181 <param name="analysis_type_selector" value="coverage"/>
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182 <output name="output_bam" file="bamtools-coverage.tab" />
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183 </test>
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184 <test>
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185 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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186 <param name="analysis_type_selector" value="header"/>
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187 <output name="output_bam" file="bamtools-header.txt" />
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188 </test>
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189 </tests>
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190 <help>
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191
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192 **What is does**
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193
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194 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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195 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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196
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197 -----
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198
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199 **Convert**
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200
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201 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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202 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
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203
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204 -----
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205
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206 **Count**
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207
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208 Counts a number of alignments in a BAM dataset(s).
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209
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210 -----
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211
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212 **Coverage**
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213
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214 Prints per-base coverage for a BAM dataset.
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215
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216 -----
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217
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218 **Header**
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219
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220 Prints header from a BAM dataset(s).
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221
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222 ------
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223
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224 **Merge**
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225
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226 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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227
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228 ------
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229
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230 **Random**
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231
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232 Grabs a specified number of random lines from BAM dataset(s).
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233
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234 ------
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235
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236 **Revert**
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237
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238 Removes duplicate marks and restores original (non-recalibrated) base qualities.
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239
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240 -----
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241
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242 .. class:: infomark
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243
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244 **More information**
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245
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246 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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247
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248 </help>
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249 <citations>
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250 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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251 </citations>
0
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252 </tool>