Mercurial > repos > iuc > mosdepth

comparison mosdepth.xml @ 3:5cd5d0947354 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit f2a83bdcd9dd514ee56a1b9e26811e65fa431c49
author iuc
date Sun, 25 Feb 2024 12:34:53 +0000
parents efd53f6ceb16
children 91d89a597aac
comparison
equal deleted inserted replaced
2:efd53f6ceb16 3:5cd5d0947354
23 <yield /> 23 <yield />
24 </valid> 24 </valid>
25 </sanitizer> 25 </sanitizer>
26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator> 26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
27 </xml> 27 </xml>
28 <token name="@TOOL_VERSION@">0.3.5</token> 28 <token name="@TOOL_VERSION@">0.3.6</token>
29 </macros> 29 </macros>
30 <requirements> 30 <requirements>
31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement> 31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
32 <requirement type="package" version="1.13">gzip</requirement> 32 <requirement type="package" version="1.13">gzip</requirement>
33 </requirements> 33 </requirements>
54 --by '$window.region_file' 54 --by '$window.region_file'
55 #end if 55 #end if
56 $per_base_coverage 56 $per_base_coverage
57 #if $advanced.options == "yes" 57 #if $advanced.options == "yes"
58 #if str($advanced.chrom) 58 #if str($advanced.chrom)
59 --chrom '$advanced.chrom' 59 --chrom '$advanced.chrom'
60 #end if 60 #end if
61 #if $advanced.exclude_flag 61 #if $advanced.exclude_flag
62 --flag $advanced.exclude_flag 62 --flag $advanced.exclude_flag
63 #end if 63 #end if
64 #if $advanced.include_flag 64 #if $advanced.include_flag
72 $advanced.use_median 72 $advanced.use_median
73 #if str($advanced.read_groups) 73 #if str($advanced.read_groups)
74 --read-groups '$read_groups' 74 --read-groups '$read_groups'
75 #end if 75 #end if
76 #if len($advanced.quantize) 76 #if len($advanced.quantize)
77 --quantize '$quant_groups_depths_str' 77 --quantize '$quant_groups_depths_str'
78 #end if
79 #if str($advanced.min_frag_len):
80 --min-frag-len $advanced.min_frag_len
81 #end if
82 #if str($advanced.max_frag_len):
83 --max-frag-len $advanced.max_frag_len
78 #end if 84 #end if
79 #end if 85 #end if
80 output input_alignment 86 output input_alignment
81 #if $per_base_coverage 87 #if $per_base_coverage
82 && gunzip output.per-base.bed.gz 88 && gunzip output.per-base.bed.gz
139 <!-- while read group IDs are not well specified in the BAM specification, they appear to be like IDs but with spaces allowed --> 145 <!-- while read group IDs are not well specified in the BAM specification, they appear to be like IDs but with spaces allowed -->
140 <expand macro="bam_identifier"> 146 <expand macro="bam_identifier">
141 <add value=" " /> 147 <add value=" " />
142 </expand> 148 </expand>
143 </param> 149 </param>
150 <param argument="--min-frag-len" type="integer" min="0" optional="true" label="Reads with a smaller insert size than this are ignored" />
151 <param argument="--max-frag-len" type="integer" min="0" optional="true" label="Reads with a larger insert size than this are ignored" />
144 <repeat name="quantize" title="Read depth thresholds for depth-defined regions"> 152 <repeat name="quantize" title="Read depth thresholds for depth-defined regions">
145 <param name="quant_group_mindepth" type="integer" min="0" value="0" label="Minimum depth for depth-defined region" help="Regions with this depth or lower will be included in this depth-defined region" /> 153 <param name="quant_group_mindepth" type="integer" min="0" value="0" label="Minimum depth for depth-defined region" help="Regions with this depth or lower will be included in this depth-defined region" />
146 <param name="quant_group_name" type="text" label="Depth-defined region name" help="Name include in BED output for regions in this depth-defined region"> 154 <param name="quant_group_name" type="text" label="Depth-defined region name" help="Name include in BED output for regions in this depth-defined region">
147 <sanitizer invalid_char=""> 155 <sanitizer invalid_char="">
148 <valid initial="string.letters,string.digits"> 156 <valid initial="string.letters,string.digits">
271 <help><![CDATA[ 279 <help><![CDATA[
272 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files. 280 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files.
273 281
274 It can compute: 282 It can compute:
275 283
276 * mean (or median) depth in fixed sized windows 284 * mean (or median) depth in fixed-sized windows
277 * mean (or median) depth in regions specified by a BED file 285 * mean (or median) depth in regions specified by a BED file
278 * per base depths 286 * per base depths
279 * a histogram of read depths 287 * a histogram of read depths
280 * the mean or median coverage histogram for windows / regions 288 * the mean or median coverage histogram for windows / regions
281 * a distribution of proportion of based covered over a particular threshold 289 * a distribution of proportion of based covered over a particular threshold
282 * a BED format report on regions that are defined by coverage thresholds 290 * a BED format report on regions that are defined by coverage thresholds
283 291
284 By default only a summary and depth histogram is computed, but the other options mentioned above can 292 By default, only a summary and depth histogram is computed, but the other options mentioned above can
285 be enabled using different options in the "Compute depth by region" selector and some of the Advanced 293 be enabled using different options in the "Compute depth by region" selector and some of the Advanced
286 options. 294 options.
287 295
288 .. _mosdepth: https://github.com/brentp/mosdepth 296 .. _mosdepth: https://github.com/brentp/mosdepth
289 ]]></help> 297 ]]></help>