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

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"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
comparison
equal deleted inserted replaced
8:cb20f99fd45b 9:1dfd95ee241e
1 <tool id="bamFilter" name="Filter" version="2.4.1"> 1 <tool id="bamFilter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>BAM datasets on a variety of attributes</description> 2 <description>BAM datasets on a variety of attributes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
39 <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to filter" /> 39 <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to filter" />
40 <repeat name="conditions" title="Condition" min="1"> 40 <repeat name="conditions" title="Condition" min="1">
41 <repeat name="filters" title="Filter" min="1"> 41 <repeat name="filters" title="Filter" min="1">
42 <conditional name="bam_property"> 42 <conditional name="bam_property">
43 <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> 43 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
44 <option value="alignmentFlag"/> 44 <option value="alignmentFlag">Alignment flag</option>
45 <option value="cigar"/> 45 <option value="cigar">CIGAR string</option>
46 <option value="insertSize"/> 46 <option value="insertSize">Insert size</option>
47 <option value="isDuplicate"/> 47 <option value="isDuplicate">Duplicate</option>
48 <option value="isFailedQC"/> 48 <option value="isFailedQC">Quality check</option>
49 <option value="isFirstMate"/> 49 <option value="isFirstMate">First mate</option>
50 <option value="isMapped"/> 50 <option value="isMapped">Mapped</option>
51 <option value="isMateMapped"/> 51 <option value="isMateMapped">Mate mapped</option>
52 <option value="isMateReverseStrand"/> 52 <option value="isMateReverseStrand">Mate is on reverse strand</option>
53 <option value="isPaired"/> 53 <option value="isPaired">Paired</option>
54 <option value="isPrimaryAlignment"/> 54 <option value="isPrimaryAlignment">Primary alignment</option>
55 <option value="isProperPair"/> 55 <option value="isProperPair">Proper pair</option>
56 <option value="isReverseStrand"/> 56 <option value="isReverseStrand">Reverse strand</option>
57 <option value="isSecondMate"/> 57 <option value="isSecondMate">Second mate</option>
58 <option selected="True" value="mapQuality"/> 58 <option selected="true" value="mapQuality">Mapping quality</option>
59 <option value="matePosition"/> 59 <option value="matePosition">Position of the mate</option>
60 <option value="mateReference"/> 60 <option value="mateReference">Reference name of the mate</option>
61 <option value="name"/> 61 <option value="name">Read name</option>
62 <option value="position"/> 62 <option value="position">Position of the read</option>
63 <option value="queryBases"/> 63 <option value="queryBases">Sequence motif</option>
64 <option value="reference"/> 64 <option value="reference">Reference name of the read</option>
65 <option value="tag"/> 65 <option value="tag">Tag</option>
66 </param> 66 </param>
67 <!-- would be fanstastic to have AND and OR constructs in when statements --> 67 <!-- would be fanstastic to have AND and OR constructs in when statements -->
68 <when value="alignmentFlag"> 68 <when value="alignmentFlag">
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"/> 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"/>
70 </when> 70 </when>
77 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid> 77 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid>
78 </sanitizer> 78 </sanitizer>
79 </param> 79 </param>
80 </when> 80 </when>
81 <when value="isDuplicate"> 81 <when value="isDuplicate">
82 <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" /> 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" />
83 </when> 83 </when>
84 <when value="isFailedQC"> 84 <when value="isFailedQC">
85 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> 85 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>
86 </when> 86 </when>
87 <when value="isFirstMate"> 87 <when value="isFirstMate">