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comparison picard_EstimateLibraryComplexity.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 f9242e01365a
comparison
equal deleted inserted replaced
20:2a17c789e0a5 21:6f9c0884a3e7
16 16
17 MIN_IDENTICAL_BASES="${min_identical_bases}" 17 MIN_IDENTICAL_BASES="${min_identical_bases}"
18 MAX_DIFF_RATE="${max_diff_rate}" 18 MAX_DIFF_RATE="${max_diff_rate}"
19 MIN_MEAN_QUALITY="${min_mean_quality}" 19 MIN_MEAN_QUALITY="${min_mean_quality}"
20 MAX_GROUP_RATIO="${max_group_ratio}" 20 MAX_GROUP_RATIO="${max_group_ratio}"
21 #import pipes 21 READ_NAME_REGEX='${ str( $read_name_regex ) }'
22 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
23 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" 22 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
24 23
25 VALIDATION_STRINGENCY="${validation_stringency}" 24 VALIDATION_STRINGENCY="${validation_stringency}"
26 QUIET=true 25 QUIET=true
27 VERBOSITY=ERROR 26 VERBOSITY=ERROR
34 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/> 33 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
35 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/> 34 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>
36 <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/> 35 <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>
37 36
38 <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]+).*."> 37 <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]+).*.">
39 <sanitizer> 38 <expand macro="sanitize_query" />
40 <valid initial="string.printable">
41 </valid>
42 </sanitizer>
43 </param> 39 </param>
44 <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"/> 40 <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"/>
45 41
46 <expand macro="VS" /> 42 <expand macro="VS" />
47 43