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comparison picard_MarkDuplicates.xml @ 17:fc288950c3b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author iuc
date Thu, 13 Apr 2017 19:09:24 -0400
parents 465cbb0cf2eb
children 7615ac66c6e5
comparison
equal deleted inserted replaced
16:6741a8ace658 17:fc288950c3b7
1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0"> 1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1">
2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> 2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
9 @symlink_element_identifier@ 9 @symlink_element_identifier@
10 picard 10 picard
11 MarkDuplicates 11 MarkDuplicates
12 12
13 INPUT='$escaped_element_identifier' 13 INPUT='$escaped_element_identifier'
14 OUTPUT="${outFile}" 14 OUTPUT='${outFile}'
15 15
16 METRICS_FILE="${metrics_file}" 16 METRICS_FILE='${metrics_file}'
17 #for $element in $comments: 17 #for $element in $comments:
18 COMMENT="${element.comment}" 18 COMMENT='${element.comment}'
19 #end for 19 #end for
20 REMOVE_DUPLICATES="${remove_duplicates}"
21 ASSUME_SORTED="${assume_sorted}"
22 20
23 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" 21 REMOVE_DUPLICATES='${remove_duplicates}'
22 ASSUME_SORTED='${assume_sorted}'
23
24 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
24 25
25 #import pipes 26 #import pipes
26 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } 27 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
27 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" 28 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
28 29
29 VALIDATION_STRINGENCY="${validation_stringency}" 30 # Optional arguments
31 #if $barcode_tag:
32 BARCODE_TAG='${barcode_tag}'
33 #end if
34
35 VALIDATION_STRINGENCY='${validation_stringency}'
30 QUIET=true 36 QUIET=true
31 VERBOSITY=ERROR 37 VERBOSITY=ERROR
32 38
33 ]]></command> 39 ]]></command>
34 <inputs> 40 <inputs>
50 <valid initial="string.printable"> 56 <valid initial="string.printable">
51 </valid> 57 </valid>
52 </sanitizer> 58 </sanitizer>
53 </param> 59 </param>
54 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> 60 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
61
62 <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/>
55 63
56 <expand macro="VS" /> 64 <expand macro="VS" />
57 65
58 </inputs> 66 </inputs>
59 67
114 The maximum offset between two duplicte clusters in order to consider them optical 122 The maximum offset between two duplicte clusters in order to consider them optical
115 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) 123 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
116 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in 124 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
117 which case 50-100 is more normal. Default value: 100. 125 which case 50-100 is more normal. Default value: 100.
118 126
127 BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.
128
119 @more_info@ 129 @more_info@
120 130
121 </help> 131 </help>
122 </tool> 132 </tool>
123 133