Mercurial > repos > devteam > bamtools_filter

annotate bamtools-filter.xml @ 10:4089f1be1a71 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author devteam
date Wed, 18 Jan 2017 11:46:59 -0500
parents c20a4a4acf3f
children 6fae66d050a7
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10
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1 <tool id="bamFilter" name="Filter" version="2.4.0">
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2 <description>BAM datasets on a variety of attributes</description>
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3 <requirements>
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4 <requirement type="package" version="2.4.0">bamtools</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 cat $script_file > $out_file2;
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9 #for $bam_count, $input_bam in enumerate( $input_bams ):
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10 ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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11 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
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12 #end for
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13 bamtools
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14 filter
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15 -script $script_file
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16 #for $bam_count, $input_bam in enumerate( $input_bams ):
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17 -in "localbam_${bam_count}.bam"
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18 #end for
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19 -out $out_file1
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20 ]]>
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21 </command>
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22 <configfiles>
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23 <configfile name="script_file">
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24 ##Sets up a json configfile for bamtools filter
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25 ##If there is more than one condition prints brackets and "filters:"
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26 #if len( $conditions ) > 1
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27 {
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28 "filters":
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29 [
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30 #end if
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31 #for $i, $c in enumerate( $conditions, start=1 )
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32 { "id": "$i",
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33 #for $j, $s in enumerate( $c.filters, start=1 )
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34 ##The if below takes care of the comma at the end of last condition within group
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35 #if $j != len( $c.filters)
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36 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
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37 #else
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38 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
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39 #end if
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40 #end for
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41 ##The if below takes care of the comma at the end of last condition within group
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42 #if $i != len( $conditions )
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43 },
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44 #else
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45 }
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46 #end if
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47 #end for
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48 #if len( $conditions ) > 1
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49 #if str( $rule_configuration.rules_selector ) == "True":
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50 ],
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51 "rule" : "${rule_configuration.rules}"
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52 #else
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53 ]
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54 #end if
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55 }
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56 #end if
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57 </configfile>
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58 </configfiles>
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59 <inputs>
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60 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
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61 <repeat name="conditions" title="Condition" min="1">
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62 <repeat name="filters" title="Filter" min="1">
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63 <conditional name="bam_property">
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64 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
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65 <option value="alignmentFlag"/>
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66 <option value="cigar"/>
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67 <option value="insertSize"/>
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68 <option value="isDuplicate"/>
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69 <option value="isFailedQC"/>
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70 <option value="isFirstMate"/>
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71 <option value="isMapped"/>
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72 <option value="isMateMapped"/>
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73 <option value="isMateReverseStrand"/>
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74 <option value="isPaired"/>
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75 <option value="isPrimaryAlignment"/>
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76 <option value="isProperPair"/>
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77 <option value="isReverseStrand"/>
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78 <option value="isSecondMate"/>
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79 <option selected="True" value="mapQuality"/>
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80 <option value="matePosition"/>
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81 <option value="mateReference"/>
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82 <option value="name"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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83 <option value="position"/>
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84 <option value="queryBases"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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85 <option value="reference"/>
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86 <option value="tag"/>
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87 </param>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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88 <!-- would be fanstastic to have AND and OR constructs in when statements -->
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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89 <when value="alignmentFlag">
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90 <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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91 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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92 <when value="cigar">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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93 <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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94 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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95 <when value="insertSize">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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96 <param name="bam_property_value" type="text" value=">=250" label="Filter on insert size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use &quot;>=250&quot;">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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97 <sanitizer invalid_char="">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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98 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid>
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99 </sanitizer>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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100 </param>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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101 </when>
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102 <when value="isDuplicate">
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103 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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104 </when>
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105 <when value="isFailedQC">
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106 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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107 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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108 <when value="isFirstMate">
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109 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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110 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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111 <when value="isMapped">
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112 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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113 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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114 <when value="isMateMapped">
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115 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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116 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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117 <when value="isMateReverseStrand">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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118 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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119 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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120 <when value="isPaired">
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121 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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122 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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123 <when value="isPrimaryAlignment">
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124 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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125 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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126 <when value="isProperPair">
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127 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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128 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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129 <when value="isReverseStrand">
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130 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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131 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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132 <when value="isSecondMate">
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133 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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134 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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135 <when value="mapQuality">
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136 <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use &quot;>=30&quot;">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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137 <sanitizer invalid_char="">
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138 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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139 </sanitizer>
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140 </param>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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141 </when>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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142 <when value="matePosition">
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143 <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use &quot;&gt;1000000&quot;">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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144 <sanitizer invalid_char="">
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145 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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146 </sanitizer>
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147 </param>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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148 </when>
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149 <when value="mateReference">
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150 <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use &quot;chr22&quot;">
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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151 <sanitizer invalid_char="">
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152 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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153 </sanitizer>
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154 </param>
4089f1be1a71 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
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155 </when>
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156 <when value="name">
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157 <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression.">
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158 <sanitizer invalid_char="">
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159 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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160 </sanitizer>
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161 </param>
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162 </when>
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163 <when value="position">
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164 <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use &quot;&gt;5000&quot;">
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165 <sanitizer invalid_char="">
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166 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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167 </sanitizer>
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168 </param>
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169 </when>
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170 <when value="queryBases">
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171 <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression">
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172 <sanitizer invalid_char="">
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173 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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174 </sanitizer>
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175 </param>
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176 </when>
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177 <when value="reference">
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178 <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression">
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179 <sanitizer invalid_char="">
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180 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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181 </sanitizer>
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182 </param>
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183 </when>
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184 <when value="tag">
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185 <param name="bam_property_value" type="text" value="NM:&gt;1" label="Filter on a particular tag" help="You can use &gt;, &lt;, =, and ! (not). Tag name and its value must be separated by &quot;:&quot;. E.g., to obtain reads with at least one mismatch use &quot;NM:&gt;1&quot;">
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186 <sanitizer invalid_char="">
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187 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!="/></valid>
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188 </sanitizer>
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189 </param>
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190 </when>
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191 </conditional>
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192 </repeat>
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193 </repeat>
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194 <conditional name="rule_configuration">
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195 <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." />
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196 <when value="false"/>
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197 <when value="true">
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198 <param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
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199 <sanitizer invalid_char="">
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200 <valid initial="string.printable"/>
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201 </sanitizer>
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202 </param>
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203 </when>
0
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204 </conditional>
10
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205 </inputs>
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206 <outputs>
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207 <data format="txt" name="out_file2" />
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208 <data format="bam" name="out_file1" />
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209 </outputs>
0
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210 <tests>
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211 <test>
9
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212 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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213 <param name="bam_property_selector" value="mapQuality"/>
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214 <param name="bam_property_value" value=">20"/>
9
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215 <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
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216 </test>
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217 </tests>
10
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218 <help>
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219 **What is does**
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220
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221 BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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222
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223 -----
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224
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225 **How it works**
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226
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227 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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228
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229 *Input BAM(s)*
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230
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231 The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter**
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232
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233 *Conditions and Filters*
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234
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235 Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below.
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236
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237 -----
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238
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239 **Example 1. Using a single filter**
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240
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241 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters).
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242 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:
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243
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244 .. image:: single-filter.png
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245
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246 -----
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247
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248 **Example 2. Using multiple filters**
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249
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250 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only.
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251 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button):
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252
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253 .. image:: multiple-filters.png
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254
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255 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering.
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256 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example.
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257
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258 -----
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259
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260 **Example 3. Complex filtering with multiple conditions**
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261
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262 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*)
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263 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*.
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264 The following screenshot expalins how this can be done:
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265
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266 .. image:: complex-filters.png
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267
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268 -----
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269
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270 **Example 4. Even more complex filtering with Rules**
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271
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272 In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering.
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273 For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such
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274 filtering will look like this::
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275
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276 !(1) &amp; (2 | 3)
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277
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278 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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279
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280 .. image:: rule.png
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281
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282 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule.
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283 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means::
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284
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285 NOT condition 1 AND (condition 2 OR condition 3)
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286
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287 -----
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288
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289 **JSON script file**
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290
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291 This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools.
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292 For instance, the example 4 looks like this in the JSON form::
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293
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294 {
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295 "filters":
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296 [
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297 { "id": "1",
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298 "tag":"NM:=0",
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299 "isReverseStrand":"false"
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300 },
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301 { "id": "2",
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302 "tag":"NM:>0",
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303 "isReverseStrand":"true"
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304 }
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305 ]
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306 }
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307
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308
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309 -----
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310
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311 **More information**
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312
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313 .. class:: infomark
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314
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315 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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316
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317
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318 </help>
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319 <citations>
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320 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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321 </citations>
0
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322 </tool>