Mercurial > repos > devteam > bamtools_filter

annotate bamtools-filter.xml @ 6:82658c080fd0 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 36169ce65193faaace8e8b999f83adf0c3d5aeba
author iuc
date Tue, 05 Jun 2018 15:29:04 -0400
parents bd735cae4ce6
children 4fe8a75334c8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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
1 <tool id="bamFilter" name="Filter" version="2.4.1">
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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 &&
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
12 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
13 ]]>
bd735cae4ce6 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 </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
15 <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
16 <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
17 <![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
18 <% 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
19 #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
20 #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
21 #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
22 #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
23 #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
24 #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
25 #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
26 #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
27 $(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
28 #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
29 #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
30 #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
31 #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
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 $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
34 ]]>
bd735cae4ce6 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 </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
36 </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
37 <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
38 <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
39 <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
40 <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
41 <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
42 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
bd735cae4ce6 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 <option 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
44 <option 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
45 <option value="insertSize"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
46 <option value="isDuplicate"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
47 <option 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
48 <option 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
49 <option 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
50 <option 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
51 <option 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
52 <option 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
53 <option 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
54 <option 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
55 <option 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
56 <option 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
57 <option selected="True" value="mapQuality"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
58 <option 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
59 <option 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
60 <option 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
61 <option 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
62 <option 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
63 <option 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
64 <option value="tag"/>
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
65 </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
66 <!-- 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
67 <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
68 <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
69 </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
70 <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
71 <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
72 </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
73 <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
74 <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
75 <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
76 <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
77 </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
78 </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
79 </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
80 <when value="isDuplicate">
bd735cae4ce6 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 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
82 </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
83 <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
84 <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
85 </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
86 <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
87 <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
88 </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
89 <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
90 <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
91 </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
92 <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
93 <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
94 </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
95 <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
96 <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
97 </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
98 <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
99 <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
100 </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
101 <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
102 <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
103 </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
104 <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
105 <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
106 </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
107 <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
108 <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
109 </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
110 <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
111 <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
112 </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
113 <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
114 <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
115 <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
116 <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
117 </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
118 </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
119 </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
120 <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
121 <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
122 <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
123 <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
124 </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
125 </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
126 </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
127 <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
128 <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
129 <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
130 <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
131 </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
132 </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
133 </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
134 <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
135 <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
136 <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
137 <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
138 </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
139 </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
140 </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
141 <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
142 <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
143 <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
144 <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
145 </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
146 </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
147 </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
148 <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
149 <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
150 <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
151 <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
152 </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
153 </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
154 </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
155 <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
156 <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
157 <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
158 <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
159 </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
160 </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
161 </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
162 <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
163 <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
164 <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
165 <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
166 </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
167 </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
168 </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
169 </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
170 </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
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 <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
173 <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
174 <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
175 <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
176 <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
177 <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
178 <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
179 </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
180 </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
181 </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
182 </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
183 </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
184 <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
185 <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
bd735cae4ce6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
devteam
parents: 4
diff changeset
186 <data name="out_file1" format="bam" label="${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
187 </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
188 <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
189 <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
190 <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
191 <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
192 <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
193 <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
194 </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
195 </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
196 <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
197 <![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
198 **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
199
bd735cae4ce6 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 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
201
bd735cae4ce6 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 **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
205
bd735cae4ce6 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 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
207
bd735cae4ce6 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 *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
209
bd735cae4ce6 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 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
211
bd735cae4ce6 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 *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
213
bd735cae4ce6 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 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
215
bd735cae4ce6 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 **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
219
bd735cae4ce6 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 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
221 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
222
bd735cae4ce6 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 .. 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
224
bd735cae4ce6 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 **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
228
bd735cae4ce6 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 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
230 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
231
bd735cae4ce6 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 .. 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
233
bd735cae4ce6 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 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
235 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
236
bd735cae4ce6 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 **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
240
bd735cae4ce6 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 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
242 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
243 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
244
bd735cae4ce6 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 .. 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
246
bd735cae4ce6 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 **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
250
bd735cae4ce6 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 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
252 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
253 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
254
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
255 !(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
256
bd735cae4ce6 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 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
258
bd735cae4ce6 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 .. 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
260
bd735cae4ce6 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 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
262 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
263
bd735cae4ce6 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 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
265
bd735cae4ce6 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 **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
269
bd735cae4ce6 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 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
271 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
272
bd735cae4ce6 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 "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
275 [
bd735cae4ce6 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 { "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
277 "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
278 "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
279 },
bd735cae4ce6 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 { "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
281 "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
282 "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
283 }
bd735cae4ce6 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 **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
291
bd735cae4ce6 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 .. 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
293
bd735cae4ce6 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 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
295 ]]>
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
296 </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
297 <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
298 <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
299 </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
300 </tool>