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annotate bamtools-filter.xml @ 10:108db6635177 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter commit 862f05b5053f55def8007194a702019418697cb5
author iuc
date Fri, 13 Jan 2023 12:17:39 +0000
parents 1dfd95ee241e
children 993b19f20c76
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108db6635177 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter commit 862f05b5053f55def8007194a702019418697cb5
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1 <tool id="bamFilter" name="Filter BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
108db6635177 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter commit 862f05b5053f55def8007194a702019418697cb5
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2 <description>datasets on a variety of attributes</description>
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3 <macros>
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4 <import>macros.xml</import>
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
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5 </macros>
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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 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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10 ln -s '${input_bam}' localbam.bam &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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11 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
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4fe8a75334c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit c72d58cbe6a99bc8f9fde26fdde45b0c222890df
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12 cat '$script_file' &&
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bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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13 bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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14 ]]>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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15 </command>
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16 <configfiles>
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17 <configfile name="script_file">
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18 <![CDATA[
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19 <% import json %>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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20 #set $config = dict()
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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21 #if $conditions:
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 $config[ 'filters' ] = []
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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23 #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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24 #set $filter = dict( id=str( $i ) )
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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25 #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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26 #set $filter[ $str( s[ 'bam_property' ][ 'bam_property_selector' ] ) ] = $str( s[ 'bam_property' ][ 'bam_property_value' ] )
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 $(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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29 #end for
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30 #if str( $rule_configuration.rules_selector ) == "true":
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31 #set $config[ 'rule' ] = str( $rule_configuration.rules )
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32 #end if
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33 #end if
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34 $json.dumps( $config, indent=4 )
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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35 ]]>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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36 </configfile>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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37 </configfiles>
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38 <inputs>
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39 <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to 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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40 <repeat name="conditions" title="Condition" min="1">
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41 <repeat name="filters" title="Filter" min="1">
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42 <conditional name="bam_property">
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43 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
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1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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44 <option value="alignmentFlag">Alignment flag</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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45 <option value="cigar">CIGAR string</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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46 <option value="insertSize">Insert size</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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47 <option value="isDuplicate">Duplicate</option>
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48 <option value="isFailedQC">Quality check</option>
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49 <option value="isFirstMate">First mate</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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50 <option value="isMapped">Mapped</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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51 <option value="isMateMapped">Mate mapped</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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52 <option value="isMateReverseStrand">Mate is on reverse strand</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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53 <option value="isPaired">Paired</option>
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54 <option value="isPrimaryAlignment">Primary alignment</option>
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55 <option value="isProperPair">Proper pair</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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56 <option value="isReverseStrand">Reverse strand</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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57 <option value="isSecondMate">Second mate</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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58 <option selected="true" value="mapQuality">Mapping quality</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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59 <option value="matePosition">Position of the mate</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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60 <option value="mateReference">Reference name of the mate</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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61 <option value="name">Read name</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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62 <option value="position">Position of the read</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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63 <option value="queryBases">Sequence motif</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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64 <option value="reference">Reference name of the read</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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65 <option value="tag">Tag</option>
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66 </param>
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67 <!-- would be fanstastic to have AND and OR constructs in when statements -->
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68 <when value="alignmentFlag">
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69 <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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70 </when>
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71 <when value="cigar">
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72 <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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73 </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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74 <when value="insertSize">
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75 <param name="bam_property_value" type="text" value="&gt;=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;&gt;=250&quot;">
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bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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76 <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
77 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><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
78 </sanitizer>
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
79 </param>
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
80 </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
81 <when value="isDuplicate">
9
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
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82 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads marked as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
5
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
83 </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
84 <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
85 <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
86 </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
87 <when value="isFirstMate">
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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88 <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
89 </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
90 <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
91 <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
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parents: 4
diff changeset
92 </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
93 <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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94 <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
95 </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
96 <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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97 <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
98 </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
99 <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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100 <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
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parents: 4
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101 </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
102 <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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103 <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
104 </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
105 <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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106 <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
107 </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
108 <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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109 <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
110 </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
111 <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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112 <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
113 </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
114 <when value="mapQuality">
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
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115 <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;&gt;=30&quot;">
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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parents: 4
diff changeset
116 <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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117 <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
118 </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
119 </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
120 </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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121 <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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122 <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
123 <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
124 <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
125 </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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126 </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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127 </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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128 <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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129 <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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diff changeset
130 <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
131 <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
132 </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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133 </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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134 </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
135 <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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136 <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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diff changeset
137 <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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138 <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
139 </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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140 </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
141 </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
142 <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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143 <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
144 <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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145 <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
146 </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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147 </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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148 </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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149 <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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150 <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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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>
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155 </when>
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156 <when value="reference">
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157 <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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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="tag">
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164 <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;">
5
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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 </conditional>
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171 </repeat>
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172 </repeat>
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173 <conditional name="rule_configuration">
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174 <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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175 <when value="false"/>
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176 <when value="true">
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177 <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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178 <sanitizer invalid_char="">
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179 <valid initial="string.printable"/>
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180 </sanitizer>
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181 </param>
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182 </when>
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183 </conditional>
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184 </inputs>
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185 <outputs>
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186 <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
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187 <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" />
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188 </outputs>
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189 <tests>
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190 <test>
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191 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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192 <param name="bam_property_selector" value="mapQuality"/>
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193 <param name="bam_property_value" value="&gt;20"/>
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194 <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
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195 </test>
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196 </tests>
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197 <help>
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198 <![CDATA[
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199 **What is does**
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200
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201 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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202
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203 -----
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204
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205 **How it works**
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206
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207 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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208
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209 *Input BAM(s)*
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210
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211 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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212
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213 *Conditions and Filters*
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214
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215 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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216
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217 -----
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218
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219 **Example 1. Using a single filter**
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220
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221 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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222 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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223
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224 .. image:: single-filter.png
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225
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226 -----
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227
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228 **Example 2. Using multiple filters**
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229
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230 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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231 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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232
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233 .. image:: multiple-filters.png
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234
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235 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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236 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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237
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238 -----
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239
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240 **Example 3. Complex filtering with multiple conditions**
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241
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242 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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243 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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244 The following screenshot expalins how this can be done:
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245
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246 .. image:: complex-filters.png
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247
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248 -----
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249
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250 **Example 4. Even more complex filtering with Rules**
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251
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252 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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253 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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254 filtering will look like this::
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255
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256 !(1) & (2 | 3)
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257
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258 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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259
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260 .. image:: rule.png
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261
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262 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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263 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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264
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265 NOT condition 1 AND (condition 2 OR condition 3)
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266
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267 -----
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268
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269 **JSON script file**
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270
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271 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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272 For instance, the example 4 looks like this in the JSON form::
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273
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274 {
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275 "filters":
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276 [
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277 { "id": "1",
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278 "tag":"NM:=0",
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279 "isReverseStrand":"false"
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280 },
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281 { "id": "2",
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282 "tag":"NM:>0",
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283 "isReverseStrand":"true"
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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
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289 -----
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290
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291 **More information**
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292
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293 .. class:: infomark
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294
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295 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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296 ]]>
5
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297 </help>
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298 <citations>
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299 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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300 </citations>
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301 </tool>