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1 <!--
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2 purpose: xml file for BAMEdit tool
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3 author: Ziru Zhou
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4 date: October, 2012
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5 -->
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6 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
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7 <requirements>
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8 <requirement type="package">samtools</requirement>
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9 </requirements>
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10 <description>Merging, splitting, filtering, and QC of BAM files</description>
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11 <command interpreter="python">bamedit.py $options_file </command>
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12 <inputs>
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13 <conditional name="input_type">
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14 <param name="input_type_selector" type="select" label="Select your BAM command">
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15 <option value="merge">Merge BAM files</option>
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16 <option value="split">Split BAM file</option>
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17 <option value="filter">Filter BAM file</option>
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18 <option value="pileup">Calculate coverage QC</option>
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19 </param>
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20
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21 <when value="merge">
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22 <param format="bam" name="input1" type="data" label="Select your first input BAM file"/>
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23 <param format="bam" name="input2" type="data" label="Select your second input BAM file"/>
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24 <param format="bam" name="input3" type="data" optional="True" label="Select your third input BAM file (optional)" help="Optional third BAM file to be merged."/>
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25 </when>
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26
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27 <when value="split">
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28 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
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29 </when>
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30
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31 <when value="filter">
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32 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
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33 <param name="quality" type="integer" min="1" value="1" label="Minimum Mapping Quality (MMQ)" help="Quality filter should be 1 or higher."/>
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34 </when>
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35
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36 <when value="pileup">
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37 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
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38 <param format="fasta" name="input2" type="data" label="Select your fasta reference file"/>
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39 <!--<param name="outopt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Alternatative output format" help="format: BAM_FILE, REFERENCE_FILE, GENOME_COVERAGE_PERCENTAGE, AVERAGE_COVERAGE_OF_BASES_COVERED"/>-->
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40 </when>
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41 </conditional>
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42
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43 <param name="output_name" type="text" value="output" size="30" label="Output file name"/>
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44 </inputs>
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45
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46 <outputs>
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47 <data format="bam" name="bamoutm" label="${output_name.value}">
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48 <filter>input_type['input_type_selector'] == 'merge'</filter>
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49 </data>
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50 <data format="bam" name="bamoutf" label="${output_name.value}">
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51 <filter> input_type['input_type_selector'] == 'filter'</filter>
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52 </data>
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53 <data format="bam" name="bamouts1" label="${output_name.value}_part1">
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54 <filter>input_type['input_type_selector'] == 'split'</filter>
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55 </data>
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56 <data format="bam" name="bamouts2" label="${output_name.value}_part2">
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57 <filter>input_type['input_type_selector'] == 'split'</filter>
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58 </data>
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59 <data format="txt" name="bamoutp" label="${output_name.value}">
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60 <filter>input_type['input_type_selector'] == 'pileup'</filter>
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61 </data>
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62 </outputs>
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63
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64 <configfiles>
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65 <configfile name="options_file"><%
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66 import simplejson
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67 %>
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68 #if str($input_type.input_type_selector) == 'merge':
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69 #if str($input_type.input3) != 'None':
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70 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2), 'input3':str($input3) }
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71 #else:
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72 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) }
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73 #end if
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74 #end if
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75 #if str($input_type.input_type_selector) == 'split':
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76 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
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77 #end if
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78 #if str($input_type.input_type_selector) == 'filter':
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79 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }
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80 #end if
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81 #if str($input_type.input_type_selector) == 'pileup':
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82 #set $__options = { 'action':str("pileup"), 'bamout':str($bamoutp), 'input1':str($input1), 'input2':str($input2), 'bamname':str($input1.name), 'refname':str($input2.name) }
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83 #end if
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84 ${ simplejson.dumps( __options )}
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85 </configfile>
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86 </configfiles>
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87 <tests>
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88 <test>
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89 <!--none -->
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90 </test>
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91 </tests>
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92
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93 <help>
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94 **What it does**
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95
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96 Simple interface to manipulate BAM files through the use of SAMtools.
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97
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98 View the original SAMtools documentation: http://samtools.sourceforge.net/
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99
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100 ------
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101
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102 **Usage**
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103
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104 **Merge BAM files**: Merges 2 or 3 input BAM files into a single BAM file.
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105
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106 **Split BAM file**: Randomly split input BAM file into 2 BAM files.
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107
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108 **Filter BAM file**: Removes aligned reads from input BAM files with mapping quality lower than entered Minimum Mapping Quality (MMQ) value.
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109
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110 **Calculate coverage QC**: Calculates QC metrics such as percentage of genome covered and average coverage of bases covered for the input BAM and reference files.
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111
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112
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113 ------
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114
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115 **Citation**
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116
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117 Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
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118
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119 Written by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
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120
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121 </help>
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122 </tool>
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