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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
author iuc
date Mon, 31 Jul 2023 06:09:19 +0000
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-1:000000000000 0:b08cd2e5e61a
1 <tool id="mosdepth" name="mosdepth" version="@TOOL_VERSION@+galaxy0" profile="21.05">
2 <description>- fast and flexible depth coverage calculation</description>
3 <macros>
4 <xml name="bam_identifier">
5 <!-- this is based on section 1.2.1 of the SAM/BAM specification https://samtools.github.io/hts-specs/SAMv1.pdf -->
6 <sanitizer invalid_char="'">
7 <valid initial="string.ascii_letters,string.digits,string.punctuation">
8 <remove value="{" />
9 <remove value="}" />
10 <remove value="=" />
11 <remove value="*" />
12 <remove value="`" />
13 <remove value=")" />
14 <remove value="&lt;" />
15 <remove value="'" />
16 <remove value='"' />
17 <remove value="(" />
18 <remove value="\" />
19 <remove value="[" />
20 <remove value="&gt;" />
21 <remove value="]" />
22 <remove value="," />
23 <yield />
24 </valid>
25 </sanitizer>
26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
27 </xml>
28 <token name="@TOOL_VERSION@">0.3.4</token>
29 </macros>
30 <requirements>
31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
32 <requirement type="package" version="1.12">gzip</requirement>
33 </requirements>
34 <command detect_errors="exit_code"><![CDATA[
35 #if $advanced.options == "yes" and len($advanced.quantize)
36 #set $quantize_depths = []
37 #for $i, $quant_group in enumerate($advanced.quantize)
38 #set $quantize_depths = $quantize_depths + [str ($quant_group.quant_group_mindepth)]
39 #set $quant_group_name = str($quant_group.quant_group_name)
40 export MOSDEPTH_Q${i}=$quant_group.quant_group_name &&
41 #end for
42 #set $quant_groups_depths_str = ":".join($quantize_depths) + ':'
43 #end if
44 ln -s '$input_alignment' input_alignment &&
45 #if $input_alignment.is_of_type('bam'):
46 ln -s '${input_alignment.metadata.bam_index}' input_alignment.bai &&
47 #elif $input_alignment.is_of_type('cram'):
48 ln -s '${input_alignment.metadata.cram_index}' input_alignment.crai &&
49 #end if
50 mosdepth -t \${GALAXY_SLOTS:-1}
51 #if $window.window_mode == 'window'
52 --by $window.window_size
53 #elif $window.window_mode == 'bed'
54 --by '$window.region_file'
55 #end if
56 $per_base_coverage
57 #if $advanced.options == "yes"
58 #if str($advanced.chrom)
59 --chrom '$advanced.chrom'
60 #end if
61 #if $advanced.exclude_flag
62 --flag $advanced.exclude_flag
63 #end if
64 #if $advanced.include_flag
65 --include-flag $advanced.include_flag
66 #end if
67 --mapq $advanced.mapq
68 $advanced.no_fast
69 #if str($advanced.thresholds)
70 --thresholds '$advanced.thresholds'
71 #end if
72 $advanced.use_median
73 #if str($advanced.read_groups)
74 --read-groups '$read_groups'
75 #end if
76 #if len($advanced.quantize)
77 --quantize '$quant_groups_depths_str'
78 #end if
79 #end if
80 output input_alignment
81 #if $per_base_coverage
82 && gunzip output.per-base.bed.gz
83 #end if
84 #if $window.window_mode == "bed" or $window.window_mode == "window"
85 && gunzip output.regions.bed.gz
86 #end if
87 #if $advanced.options == "yes"
88 #if str($advanced.thresholds)
89 && gunzip output.thresholds.bed.gz
90 #end if
91 #if len($advanced.quantize)
92 && gunzip output.quantized.bed.gz
93 #end if
94 #end if
95 ]]></command>
96 <inputs>
97 <param name="input_alignment" type="data" format="bam,cram" label="Input BAM (or CRAM)" help="BAM or CRAM format mapped reads" />
98 <param argument="--no-per-base" name="per_base_coverage" type="boolean" truevalue="" falsevalue="--no-per-base" checked="false" label="Output per base depth" help="Skipping depth output for individual bases substantially decreases runtime" />
99 <conditional name="window">
100 <param name="window_mode" type="select" label="Compute depth by region" help="A BED file or window size can be provided to compute average depth by region">
101 <option value="no">Don't compute depth by region</option>
102 <option value="window">Compute average depth using a fixed size window</option>
103 <option value="bed">Compute depth in regions specified by a BED file</option>
104 </param>
105 <when value="no">
106 </when>
107 <when value="window">
108 <param name="window_size" type="integer" min="2" value="400" label="Window size for region calculation" help="Average depth will be computed for non-overlapping regions of this size" />
109 </when>
110 <when value="bed">
111 <param name="region_file" type="data" format="bed" label="BED file specifying regions" help="Average depth will be computed for regions specified in the BED file. If the BED file has a 4th column, it is used for the region name" />
112 </when>
113 </conditional>
114 <conditional name="advanced">
115 <param name="options" type="select" label="Advanced Options">
116 <option value="no" selected="true">Hide Advanced Options</option>
117 <option value="yes">Show Advanced Options</option>
118 </param>
119 <when value="no">
120 </when>
121 <when value="yes">
122 <param argument="--chrom" type="text" label="Restrict depth calculations to chromosome" optional="true" help="Enter a chromosome name to only count depth for reads mapping to this chromosome">
123 <expand macro="bam_identifier" />
124 </param>
125 <param argument="--flag" name="exclude_flag" type="integer" min="0" value="0" label="Exclude reads with these bits set in FLAG" help="Exclude reads where any of these bits are set in the value of the read flags column" />
126 <param argument="--include-flag" type="integer" min="1" optional="true" label="Only include reads with these bits set in FLAG" help="Only include reads where any of these bits are set in the value of the read flags column" />
127 <param argument="--fast-mode" name="no_fast" type="boolean" truevalue="" falsevalue="-x" label="Disable fast mode" help="Fast mode doesn't look up internal cigar operations or correct mate overlaps. Disabling it is not recommended" />
128 <param argument="--mapq" type="integer" min="0" value="0" label="Minimum mapping quality" help="Reads with a mapping quality lower than this value are ignored" />
129 <param argument="--thresholds" type="text" value="" label="Specify thresholds for output when using region output" help="The number of bases covered by these thresholds will be reported. Multiple thresholds can be separated by commas">
130 <sanitizer invalid_char="">
131 <valid initial="string.digits">
132 <add value="," />
133 </valid>
134 </sanitizer>
135 <validator type="regex">[0-9,]*</validator>
136 </param>
137 <param argument="--use-median" type="boolean" truevalue="--use-median" falsevalue="" checked="false" label="Use median depth of region" help="When computing depth of region, use median of depth rather than mean" />
138 <param argument="--read-groups" type="text" value="" label="" help="only calculate depth for these comma-separated read groups IDs">
139 <!-- 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">
141 <add value=" " />
142 </expand>
143 </param>
144 <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" />
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">
147 <sanitizer invalid_char="">
148 <valid initial="string.letters,string.digits">
149 <add value="_" />
150 </valid>
151 </sanitizer>
152 <validator type="regex">[0-9a-zA-Z_]*</validator>
153 </param>
154 </repeat>
155 </when>
156 </conditional>
157 </inputs>
158 <outputs>
159 <data name="output_global_dist" format="tabular" from_work_dir="output.mosdepth.global.dist.txt" label="mosdepth depth distribution on ${on_string}" />
160 <data name="output_summary" format="tabular" from_work_dir="output.mosdepth.summary.txt" label="mosdepth summary on ${on_string}">
161 <actions>
162 <action type="metadata" name="column_names" default="chrom,length,bases,mean,min,max" />
163 </actions>
164 </data>
165 <data name="output_region_dist" format="tabular" from_work_dir="output.mosdepth.region.dist.txt" label="mosdepth region depth distribution on ${on_string}">
166 <filter>window['window_mode'] == "bed" or window['window_mode'] == "window"</filter>
167 </data>
168 <data name="output_per_base_depth" format="bedgraph" from_work_dir="output.per-base.bed" label="mosdepth per base depth on ${on_string}">
169 <filter>per_base_coverage</filter>
170 </data>
171 <data name="output_regions_bed" format="bed" from_work_dir="output.regions.bed" label="mosdepth regions BED on ${on_string}">
172 <filter>window['window_mode'] == "bed" or window['window_mode'] == "window"</filter>
173 </data>
174 <data name="output_quantized_bed" format="bed" from_work_dir="output.quantized.bed" label="mosdepth quantized BED on ${on_string}">
175 <filter>advanced['options'] == "yes" and len(advanced['quantize'])</filter>
176 </data>
177 <data name="output_thresholds_bed" format="bed" from_work_dir="output.thresholds.bed" label="mosdepth thresholds BED on ${on_string}">
178 <filter>advanced['options'] == "yes" and advanced['thresholds']</filter>
179 </data>
180 </outputs>
181 <tests>
182 <!-- test 1 -->
183 <test expect_num_outputs="2">
184 <param name="input_alignment" value="input.bam" ftype="bam" />
185 <output name="output_summary" file="output_summary.tabular" ftype="tabular" />
186 <output name="output_global_dist" file="output_distribution.tabular" ftype="tabular" />
187 </test>
188 <!-- test 2 -->
189 <test expect_num_outputs="3">
190 <param name="input_alignment" value="input.bam" ftype="bam" />
191 <param name="per_base_coverage" value="True" />
192 <output name="output_per_base_depth" file="output_per_base_depth.bed" ftype="bedgraph" />
193 </test>
194 <!-- test 3 -->
195 <test expect_num_outputs="4">
196 <param name="input_alignment" value="input.bam" ftype="bam" />
197 <conditional name="window">
198 <param name="window_mode" value="bed" />
199 <param name="region_file" value="input_regions.bed" ftype="bed" />
200 </conditional>
201 <output name="output_region_dist" file="output_region_distribution_bed.tabular" ftype="tabular" />
202 <output name="output_summary" file="output_region_summary.tabular" ftype="tabular" />
203 <output name="output_regions_bed" file="output_region_depths.bed" ftype="bed" />
204 </test>
205 <!-- test 4 -->
206 <test expect_num_outputs="4 ">
207 <param name="input_alignment" value="input.bam" ftype="bam" />
208 <conditional name="window">
209 <param name="window_mode" value="window" />
210 <param name="window_size" value="200" />
211 </conditional>
212 <output name="output_region_dist" file="output_region_distribution.tabular" ftype="tabular" />
213 <output name="output_summary" file="output_region_summary_windowed.tabular" ftype="tabular" />
214 <output name="output_regions_bed" file="output_window_depths.bed" ftype="bed" />
215 </test>
216 <!-- test 5 -->
217 <test expect_num_outputs="4">
218 <param name="input_alignment" value="input.bam" ftype="bam" />
219 <conditional name="window">
220 <param name="window_mode" value="window" />
221 <param name="window_size" value="200" />
222 </conditional>
223 <conditional name="advanced">
224 <param name="options" value="yes" />
225 <param name="use_median" value="yes" />
226 </conditional>
227 <output name="output_region_dist" file="output_region_distribution_median.tabular" ftype="tabular" />
228 <output name="output_summary" file="output_region_summary_windowed_median.tabular" ftype="tabular" />
229 <output name="output_regions_bed" file="output_window_depths_median.bed" ftype="bed" />
230 </test>
231 <!-- test 6 -->
232 <test expect_num_outputs="3">
233 <param name="input_alignment" value="input.bam" ftype="bam" />
234 <conditional name="advanced">
235 <param name="options" value="yes" />
236 <repeat name="quantize">
237 <param name="quant_group_mindepth" value="0" />
238 <param name="quant_group_name" value="NO_COVERAGE" />
239 </repeat>
240 <repeat name="quantize">
241 <param name="quant_group_mindepth" value="1" />
242 <param name="quant_group_name" value="LOW_COVERAGE" />
243 </repeat>
244 <repeat name="quantize">
245 <param name="quant_group_mindepth" value="20" />
246 <param name="quant_group_name" value="SUFFICIENT_COVERAGE" />
247 </repeat>
248 </conditional>
249 <output name="output_quantized_bed" file="output_quantized.bed" ftype="bed" />
250 </test>
251 <!-- test 7 -->
252 <test expect_num_outputs="5">
253 <param name="input_alignment" value="input.bam" ftype="bam" />
254 <conditional name="window">
255 <param name="window_mode" value="bed" />
256 <param name="region_file" value="input_regions.bed" ftype="bed" />
257 </conditional>
258 <conditional name="advanced">
259 <param name="options" value="yes" />
260 <param name="thresholds" value="20,40" />
261 </conditional>
262 <output name="output_thresholds_bed" file="output_thresholds.bed" ftype="bed" />
263 </test>
264 <!-- test 7 -->
265 <test expect_num_outputs="2">
266 <param name="input_alignment" value="input.cram" ftype="cram" />
267 <output name="output_summary" file="output_summary.tabular" ftype="tabular" />
268 <output name="output_global_dist" file="output_distribution.tabular" ftype="tabular" />
269 </test>
270 </tests>
271 <help><![CDATA[
272 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files.
273
274 It can compute:
275
276 * mean (or median) depth in fixed sized windows
277 * mean (or median) depth in regions specified by a BED file
278 * per base depths
279 * a histogram of read depths
280 * the mean or median coverage histogram for windows / regions
281 * a distribution of proportion of based covered over a particular threshold
282 * a BED format report on regions that are defined by coverage thresholds
283
284 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
286 options.
287
288 .. _mosdepth: https://github.com/brentp/mosdepth
289 ]]></help>
290 <citations>
291 <citation type="doi">10.1093/bioinformatics/btx699</citation>
292 </citations>
293 </tool>