Mercurial > repos > devteam > bamtools_filter

annotate bamtools-filter.xml @ 5:bd735cae4ce6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
author devteam
date Thu, 25 May 2017 11:49:34 -0400
parents 3213c223678c
children 82658c080fd0
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5
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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1 <tool id="bamFilter" name="Filter" version="2.4.1">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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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 cp '$script_file' '$out_file2' &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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9 ln -s '${input_bam}' localbam.bam &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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10 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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11 bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <configfile name="script_file">
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16 <![CDATA[
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17 <% import json %>
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18 #set $config = dict()
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19 #if $conditions:
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20 #set $config[ 'filters' ] = []
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21 #for $i, $condition in enumerate( $conditions, start=1 ):
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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22 #set $filter = dict( id=str( $i ) )
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23 #for $j, $s in enumerate( $condition.filters, start=1 ):
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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24 #set $filter[ $str( s[ 'bam_property' ][ 'bam_property_selector' ] ) ] = $str( s[ 'bam_property' ][ 'bam_property_value' ] )
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25 #end for
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26 $(config[ 'filters' ].append( $filter ))
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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27 #end for
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28 #if str( $rule_configuration.rules_selector ) == "true":
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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29 #set $config[ 'rule' ] = $rule_configuration.rules
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30 #end if
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31 #end if
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32 $json.dumps( $config, indent=4 )
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33 ]]>
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34 </configfile>
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35 </configfiles>
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36 <inputs>
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37 <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to filter" />
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38 <repeat name="conditions" title="Condition" min="1">
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39 <repeat name="filters" title="Filter" min="1">
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40 <conditional name="bam_property">
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41 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
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42 <option value="alignmentFlag"/>
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43 <option value="cigar"/>
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44 <option value="insertSize"/>
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45 <option value="isDuplicate"/>
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46 <option value="isFailedQC"/>
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47 <option value="isFirstMate"/>
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48 <option value="isMapped"/>
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49 <option value="isMateMapped"/>
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50 <option value="isMateReverseStrand"/>
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51 <option value="isPaired"/>
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52 <option value="isPrimaryAlignment"/>
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53 <option value="isProperPair"/>
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54 <option value="isReverseStrand"/>
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55 <option value="isSecondMate"/>
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56 <option selected="True" value="mapQuality"/>
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57 <option value="matePosition"/>
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58 <option value="mateReference"/>
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59 <option value="name"/>
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60 <option value="position"/>
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61 <option value="queryBases"/>
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62 <option value="reference"/>
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63 <option value="tag"/>
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64 </param>
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65 <!-- would be fanstastic to have AND and OR constructs in when statements -->
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66 <when value="alignmentFlag">
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67 <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"/>
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68 </when>
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69 <when value="cigar">
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70 <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
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71 </when>
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72 <when value="insertSize">
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73 <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;">
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74 <sanitizer invalid_char="">
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75 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid>
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76 </sanitizer>
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77 </param>
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78 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
79 <when value="isDuplicate">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
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80 <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" />
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
81 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
82 <when value="isFailedQC">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
83 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
84 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
85 <when value="isFirstMate">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
86 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
87 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
88 <when value="isMapped">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
89 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
90 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
91 <when value="isMateMapped">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
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92 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
93 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
94 <when value="isMateReverseStrand">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
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95 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
96 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
97 <when value="isPaired">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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98 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
99 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
100 <when value="isPrimaryAlignment">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
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101 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
102 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
103 <when value="isProperPair">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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104 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
105 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
106 <when value="isReverseStrand">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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107 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
108 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
109 <when value="isSecondMate">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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110 <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"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
111 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
112 <when value="mapQuality">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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113 <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;">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
114 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
115 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
116 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
117 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
118 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
119 <when value="matePosition">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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120 <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;">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
121 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
122 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
123 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
124 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
125 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
126 <when value="mateReference">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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127 <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;">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
128 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
129 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
130 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
131 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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132 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
133 <when value="name">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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134 <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression.">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
135 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
136 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
137 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
138 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
139 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
140 <when value="position">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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141 <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;">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
142 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
143 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
144 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
145 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
146 </when>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
147 <when value="queryBases">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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148 <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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parents: 4
diff changeset
149 <sanitizer invalid_char="">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
150 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
151 </sanitizer>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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diff changeset
152 </param>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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153 </when>
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154 <when value="reference">
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155 <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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156 <sanitizer invalid_char="">
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157 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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158 </sanitizer>
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159 </param>
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160 </when>
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161 <when value="tag">
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162 <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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163 <sanitizer invalid_char="">
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164 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!="/></valid>
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165 </sanitizer>
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166 </param>
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167 </when>
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168 </conditional>
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169 </repeat>
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170 </repeat>
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171 <conditional name="rule_configuration">
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172 <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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173 <when value="false"/>
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174 <when value="true">
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175 <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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176 <sanitizer invalid_char="">
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177 <valid initial="string.printable"/>
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178 </sanitizer>
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179 </param>
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180 </when>
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181 </conditional>
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182 </inputs>
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183 <outputs>
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184 <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
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185 <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" />
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186 </outputs>
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187 <tests>
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188 <test>
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189 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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190 <param name="bam_property_selector" value="mapQuality"/>
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191 <param name="bam_property_value" value=">20"/>
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192 <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
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193 </test>
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194 </tests>
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195 <help>
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196 **What is does**
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197
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198 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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199
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200 -----
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201
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202 **How it works**
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203
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204 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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205
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206 *Input BAM(s)*
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207
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208 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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209
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210 *Conditions and Filters*
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211
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212 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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213
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214 -----
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215
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216 **Example 1. Using a single filter**
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217
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218 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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219 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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220
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221 .. image:: single-filter.png
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222
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223 -----
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224
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225 **Example 2. Using multiple filters**
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226
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227 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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228 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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229
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230 .. image:: multiple-filters.png
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231
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232 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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233 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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234
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235 -----
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236
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237 **Example 3. Complex filtering with multiple conditions**
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238
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239 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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240 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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241 The following screenshot expalins how this can be done:
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242
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243 .. image:: complex-filters.png
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244
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245 -----
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246
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247 **Example 4. Even more complex filtering with Rules**
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248
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249 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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250 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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251 filtering will look like this::
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252
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253 !(1) &amp; (2 | 3)
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254
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255 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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256
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257 .. image:: rule.png
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258
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259 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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260 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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261
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262 NOT condition 1 AND (condition 2 OR condition 3)
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263
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264 -----
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265
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266 **JSON script file**
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267
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268 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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269 For instance, the example 4 looks like this in the JSON form::
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270
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271 {
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272 "filters":
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273 [
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274 { "id": "1",
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275 "tag":"NM:=0",
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276 "isReverseStrand":"false"
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277 },
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278 { "id": "2",
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279 "tag":"NM:>0",
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280 "isReverseStrand":"true"
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281 }
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282 ]
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283 }
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284
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285
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286 -----
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287
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288 **More information**
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289
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290 .. class:: infomark
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291
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292 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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293
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294
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295 </help>
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296 <citations>
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297 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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298 </citations>
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299 </tool>