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comparison picard_MarkDuplicates.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 7d34178f2812
comparison
equal deleted inserted replaced
20:2a17c789e0a5 21:6f9c0884a3e7
22 REMOVE_DUPLICATES='${remove_duplicates}' 22 REMOVE_DUPLICATES='${remove_duplicates}'
23 ASSUME_SORTED='${assume_sorted}' 23 ASSUME_SORTED='${assume_sorted}'
24 24
25 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' 25 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
26 26
27 #import pipes
28 #if $read_name_regex: 27 #if $read_name_regex:
29 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) } 28 READ_NAME_REGEX='${ str( $read_name_regex ) }'
30 #end if 29 #end if
31 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' 30 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
32 31
33 # Optional arguments 32 # Optional arguments
34 #if $barcode_tag: 33 #if $barcode_tag:
53 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> 52 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
54 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option> 53 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
55 </param> 54 </param>
56 55
57 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)"> 56 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)">
58 57 <expand macro="sanitize_query" />
59 <sanitizer>
60 <valid initial="string.printable">
61 </valid>
62 </sanitizer>
63 </param> 58 </param>
64 <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"/> 59 <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"/>
65 60
66 <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."/> 61 <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."/>
67 62