Mercurial > repos > devteam > picard

comparison picard_MarkDuplicatesWithMateCigar.xml @ 21:6f9c0884a3e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
author iuc
date Tue, 16 Oct 2018 11:49:10 -0400
parents 2a17c789e0a5
children 881d7645d1bf
comparison
equal deleted inserted replaced
20:2a17c789e0a5 21:6f9c0884a3e7
24 REMOVE_DUPLICATES="${remove_duplicates}" 24 REMOVE_DUPLICATES="${remove_duplicates}"
25 ASSUME_SORTED="${assume_sorted}" 25 ASSUME_SORTED="${assume_sorted}"
26 26
27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" 27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
28 28
29 #import pipes 29 READ_NAME_REGEX='${ str( $read_name_regex ) }'
30 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
31 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" 30 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
32 31
33 32
34 BLOCK_SIZE=100000 33 BLOCK_SIZE=100000
35 VALIDATION_STRINGENCY="${validation_stringency}" 34 VALIDATION_STRINGENCY="${validation_stringency}"
52 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> 51 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
53 </param> 52 </param>
54 53
55 54
56 <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> 55 <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
57 <sanitizer> 56 <expand macro="sanitize_query" />
58 <valid initial="string.printable">
59 </valid>
60 </sanitizer>
61 </param> 57 </param>
62 <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"/> 58 <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"/>
63 59
64 <expand macro="VS" /> 60 <expand macro="VS" />
65 61