Mercurial > repos > devteam > bamtools_filter

annotate bamtools-filter.xml @ 9:1dfd95ee241e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author iuc
date Sat, 27 Nov 2021 10:02:24 +0000
parents 4fe8a75334c8
children 108db6635177
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
1 <tool id="bamFilter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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
2 <description>BAM datasets on a variety of attributes</description>
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
3 <macros>
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
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
iuc
parents: 5
diff changeset
5 </macros>
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
6 <expand macro="requirements" />
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
7 <command detect_errors="exit_code">
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
8 <![CDATA[
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
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
devteam
parents: 4
diff changeset
10 ln -s '${input_bam}' localbam.bam &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
11 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
7
4fe8a75334c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit c72d58cbe6a99bc8f9fde26fdde45b0c222890df
iuc
parents: 6
diff changeset
12 cat '$script_file' &&
5
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
13 bamtools filter -script '$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
devteam
parents: 4
diff changeset
14 ]]>
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
15 </command>
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
16 <configfiles>
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
17 <configfile name="script_file">
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
18 <![CDATA[
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
19 <% import json %>
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
20 #set $config = dict()
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
21 #if $conditions:
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
22 #set $config[ 'filters' ] = []
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
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
27 #end for
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
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
devteam
parents: 4
diff changeset
29 #end for
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
30 #if str( $rule_configuration.rules_selector ) == "true":
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
31 #set $config[ 'rule' ] = str( $rule_configuration.rules )
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
32 #end if
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
33 #end if
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
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
devteam
parents: 4
diff changeset
35 ]]>
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
36 </configfile>
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
37 </configfiles>
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
38 <inputs>
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
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
devteam
parents: 4
diff changeset
40 <repeat name="conditions" title="Condition" min="1">
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
41 <repeat name="filters" title="Filter" min="1">
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
42 <conditional name="bam_property">
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
43 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
9
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
47 <option value="isDuplicate">Duplicate</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
48 <option value="isFailedQC">Quality check</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
53 <option value="isPaired">Paired</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
54 <option value="isPrimaryAlignment">Primary alignment</option>
1dfd95ee241e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
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"
iuc
parents: 7
diff changeset
65 <option value="tag">Tag</option>
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
66 </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
67 <!-- would be fanstastic to have AND and OR constructs in when statements -->
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
68 <when value="alignmentFlag">
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
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"/>
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
70 </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
71 <when value="cigar">
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
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
devteam
parents: 4
diff changeset
73 </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
74 <when value="insertSize">
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
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;">
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
76 <sanitizer invalid_char="">
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
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
diff changeset
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
101 </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
102 <when value="isPrimaryAlignment">
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 <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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
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
parents: 5
diff changeset
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
121 <when value="matePosition">
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
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
devteam
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
devteam
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
devteam
parents: 4
diff changeset
126 </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
127 </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
128 <when value="mateReference">
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
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
devteam
parents: 4
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
devteam
parents: 4
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
devteam
parents: 4
diff changeset
132 </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
133 </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
134 </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
135 <when value="name">
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
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
devteam
parents: 4
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
139 </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
140 </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
141 </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
142 <when value="position">
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
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
devteam
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
devteam
parents: 4
diff changeset
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
devteam
parents: 4
diff changeset
146 </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
147 </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
148 </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
149 <when value="queryBases">
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
150 <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
devteam
parents: 4
diff changeset
151 <sanitizer invalid_char="">
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
152 <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
153 </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
154 </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
155 </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
156 <when value="reference">
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
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">
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
158 <sanitizer invalid_char="">
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
159 <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
160 </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
161 </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
162 </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
163 <when value="tag">
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
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
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
165 <sanitizer invalid_char="">
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
166 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!=+-"/></valid>
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
167 </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
168 </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
169 </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
170 </conditional>
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
171 </repeat>
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
172 </repeat>
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
173 <conditional name="rule_configuration">
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
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." />
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
175 <when value="false"/>
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
176 <when value="true">
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
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." >
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
178 <sanitizer invalid_char="">
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
179 <valid initial="string.printable"/>
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
180 </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
181 </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
182 </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
183 </conditional>
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
184 </inputs>
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
185 <outputs>
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
186 <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
187 <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" />
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
188 </outputs>
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
189 <tests>
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
190 <test>
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
191 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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
192 <param name="bam_property_selector" value="mapQuality"/>
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
193 <param name="bam_property_value" value="&gt;20"/>
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
194 <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
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
195 </test>
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
196 </tests>
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
197 <help>
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
198 <![CDATA[
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
199 **What is does**
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
200
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
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).
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
202
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
203 -----
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
204
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
205 **How it works**
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
206
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
207 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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
208
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
209 *Input BAM(s)*
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
210
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
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**
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
212
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
213 *Conditions and Filters*
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
214
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
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.
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
216
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
217 -----
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
218
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
219 **Example 1. Using a single filter**
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
220
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
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).
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
222 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:
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
223
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
224 .. image:: single-filter.png
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
225
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
226 -----
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
227
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
228 **Example 2. Using multiple filters**
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
229
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
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.
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
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):
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
232
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
233 .. image:: multiple-filters.png
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
234
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
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.
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
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.
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
237
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
238 -----
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
239
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
240 **Example 3. Complex filtering with multiple conditions**
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
241
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
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*)
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
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*.
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
244 The following screenshot expalins how this can be done:
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
245
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
246 .. image:: complex-filters.png
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
247
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
248 -----
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
249
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
250 **Example 4. Even more complex filtering with Rules**
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
251
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
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.
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
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
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
254 filtering will look like this::
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
255
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
256 !(1) & (2 | 3)
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
257
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
258 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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
259
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
260 .. image:: rule.png
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
261
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
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.
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
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::
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
264
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
265 NOT condition 1 AND (condition 2 OR condition 3)
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
266
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
267 -----
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
268
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
269 **JSON script file**
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
270
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
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.
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
272 For instance, the example 4 looks like this in the JSON form::
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
273
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
274 {
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
275 "filters":
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
276 [
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
277 { "id": "1",
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
278 "tag":"NM:=0",
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
279 "isReverseStrand":"false"
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
280 },
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
281 { "id": "2",
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
282 "tag":"NM:>0",
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
283 "isReverseStrand":"true"
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
284 }
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
285 ]
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
286 }
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
287
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
288
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
289 -----
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
290
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
291 **More information**
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
292
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
293 .. class:: infomark
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
294
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
295 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
6
82658c080fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
iuc
parents: 5
diff changeset
296 ]]>
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
297 </help>
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
298 <citations>
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
299 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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
300 </citations>
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
301 </tool>