Mercurial > repos > iuc > mosdepth

annotate mosdepth.xml @ 1:a387f00796c0 draft default tip

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/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
author iuc
date Mon, 10 Nov 2025 12:15:26 +0000
parents b08cd2e5e61a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
1 <tool id="mosdepth" name="mosdepth" version="@TOOL_VERSION@+galaxy0" profile="21.05">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
2 <description>- fast and flexible depth coverage calculation</description>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
3 <macros>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
4 <xml name="bam_identifier">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
5 <!-- this is based on section 1.2.1 of the SAM/BAM specification https://samtools.github.io/hts-specs/SAMv1.pdf -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
6 <sanitizer invalid_char="'">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
7 <valid initial="string.ascii_letters,string.digits,string.punctuation">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
8 <remove value="{" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
9 <remove value="}" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
10 <remove value="=" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
11 <remove value="*" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
12 <remove value="`" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
13 <remove value=")" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
14 <remove value="&lt;" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
15 <remove value="'" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
16 <remove value='"' />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
17 <remove value="(" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
18 <remove value="\" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
19 <remove value="[" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
20 <remove value="&gt;" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
21 <remove value="]" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
22 <remove value="," />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
23 <yield />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
24 </valid>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
25 </sanitizer>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
27 </xml>
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
28 <token name="@TOOL_VERSION@">0.3.12</token>
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
29 </macros>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
30 <requirements>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
32 <requirement type="package" version="1.14">gzip</requirement>
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
33 </requirements>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
34 <command detect_errors="exit_code"><![CDATA[
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
35 #if $advanced.options == "yes" and len($advanced.quantize)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
36 #set $quantize_depths = []
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
37 #for $i, $quant_group in enumerate($advanced.quantize)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
38 #set $quantize_depths = $quantize_depths + [str ($quant_group.quant_group_mindepth)]
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
39 #set $quant_group_name = str($quant_group.quant_group_name)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
40 export MOSDEPTH_Q${i}=$quant_group.quant_group_name &&
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
41 #end for
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
42 #set $quant_groups_depths_str = ":".join($quantize_depths) + ':'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
43 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
44 ln -s '$input_alignment' input_alignment &&
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
45 #if $input_alignment.is_of_type('bam'):
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
46 ln -s '${input_alignment.metadata.bam_index}' input_alignment.bai &&
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
47 #elif $input_alignment.is_of_type('cram'):
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
48 ln -s '${input_alignment.metadata.cram_index}' input_alignment.crai &&
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
49 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
50 mosdepth -t \${GALAXY_SLOTS:-1}
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
51 #if $window.window_mode == 'window'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
52 --by $window.window_size
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
53 #elif $window.window_mode == 'bed'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
54 --by '$window.region_file'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
55 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
56 $per_base_coverage
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
57 #if $advanced.options == "yes"
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
58 #if str($advanced.chrom)
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
59 --chrom '$advanced.chrom'
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
60 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
61 #if $advanced.exclude_flag
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
62 --flag $advanced.exclude_flag
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
63 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
64 #if $advanced.include_flag
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
65 --include-flag $advanced.include_flag
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
66 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
67 --mapq $advanced.mapq
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
68 $advanced.no_fast
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
69 $advanced.fragment_mode
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
70 #if str($advanced.thresholds)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
71 --thresholds '$advanced.thresholds'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
72 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
73 $advanced.use_median
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
74 #if str($advanced.read_groups)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
75 --read-groups '$read_groups'
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
76 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
77 #if len($advanced.quantize)
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
78 --quantize '$quant_groups_depths_str'
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
79 #end if
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
80 #if str($advanced.min_frag_len):
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
81 --min-frag-len $advanced.min_frag_len
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
82 #end if
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
83 #if str($advanced.max_frag_len):
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
84 --max-frag-len $advanced.max_frag_len
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
85 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
86 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
87 output input_alignment
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
88 #if $per_base_coverage
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
89 && gunzip output.per-base.bed.gz
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
90 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
91 #if $window.window_mode == "bed" or $window.window_mode == "window"
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
92 && gunzip output.regions.bed.gz
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
93 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
94 #if $advanced.options == "yes"
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
95 #if str($advanced.thresholds)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
96 && gunzip output.thresholds.bed.gz
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
97 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
98 #if len($advanced.quantize)
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
99 && gunzip output.quantized.bed.gz
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
100 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
101 #end if
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
102 ]]></command>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
103 <inputs>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
104 <param name="input_alignment" type="data" format="bam,cram" label="Input BAM (or CRAM)" help="BAM or CRAM format mapped reads" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
105 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
106 <conditional name="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
107 <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">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
108 <option value="no">Don't compute depth by region</option>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
109 <option value="window">Compute average depth using a fixed size window</option>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
110 <option value="bed">Compute depth in regions specified by a BED file</option>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
111 </param>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
112 <when value="no">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
113 </when>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
114 <when value="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
115 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
116 </when>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
117 <when value="bed">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
118 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
119 </when>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
120 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
121 <conditional name="advanced">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
122 <param name="options" type="select" label="Advanced Options">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
123 <option value="no" selected="true">Hide Advanced Options</option>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
124 <option value="yes">Show Advanced Options</option>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
125 </param>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
126 <when value="no">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
127 </when>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
128 <when value="yes">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
129 <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">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
130 <expand macro="bam_identifier" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
131 </param>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
132 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
133 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
134 <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" />
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
135 <param argument="--fragment-mode" type="boolean" truevalue="--fragment-mode" falsevalue="" checked="false" label="Use fragment mode" help="Count the coverage of the full fragment including the full insert (proper pairs only). Note that you can use either of fast mode or fragment mode, but not both"/>
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
136 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
137 <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">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
138 <sanitizer invalid_char="">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
139 <valid initial="string.digits">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
140 <add value="," />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
141 </valid>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
142 </sanitizer>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
143 <validator type="regex">[0-9,]*</validator>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
144 </param>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
145 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
146 <param argument="--read-groups" type="text" value="" label="" help="only calculate depth for these comma-separated read groups IDs">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
147 <!-- while read group IDs are not well specified in the BAM specification, they appear to be like IDs but with spaces allowed -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
148 <expand macro="bam_identifier">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
149 <add value=" " />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
150 </expand>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
151 </param>
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
152 <param argument="--min-frag-len" type="integer" min="0" optional="true" label="Reads with a smaller insert size than this are ignored" />
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
153 <param argument="--max-frag-len" type="integer" min="0" optional="true" label="Reads with a larger insert size than this are ignored" />
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
154 <repeat name="quantize" title="Read depth thresholds for depth-defined regions">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
155 <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" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
156 <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">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
157 <sanitizer invalid_char="">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
158 <valid initial="string.letters,string.digits">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
159 <add value="_" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
160 </valid>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
161 </sanitizer>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
162 <validator type="regex">[0-9a-zA-Z_]*</validator>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
163 </param>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
164 </repeat>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
165 </when>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
166 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
167 </inputs>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
168 <outputs>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
169 <data name="output_global_dist" format="tabular" from_work_dir="output.mosdepth.global.dist.txt" label="mosdepth depth distribution on ${on_string}" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
170 <data name="output_summary" format="tabular" from_work_dir="output.mosdepth.summary.txt" label="mosdepth summary on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
171 <actions>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
172 <action type="metadata" name="column_names" default="chrom,length,bases,mean,min,max" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
173 </actions>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
174 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
175 <data name="output_region_dist" format="tabular" from_work_dir="output.mosdepth.region.dist.txt" label="mosdepth region depth distribution on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
176 <filter>window['window_mode'] == "bed" or window['window_mode'] == "window"</filter>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
177 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
178 <data name="output_per_base_depth" format="bedgraph" from_work_dir="output.per-base.bed" label="mosdepth per base depth on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
179 <filter>per_base_coverage</filter>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
180 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
181 <data name="output_regions_bed" format="bed" from_work_dir="output.regions.bed" label="mosdepth regions BED on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
182 <filter>window['window_mode'] == "bed" or window['window_mode'] == "window"</filter>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
183 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
184 <data name="output_quantized_bed" format="bed" from_work_dir="output.quantized.bed" label="mosdepth quantized BED on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
185 <filter>advanced['options'] == "yes" and len(advanced['quantize'])</filter>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
186 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
187 <data name="output_thresholds_bed" format="bed" from_work_dir="output.thresholds.bed" label="mosdepth thresholds BED on ${on_string}">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
188 <filter>advanced['options'] == "yes" and advanced['thresholds']</filter>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
189 </data>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
190 </outputs>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
191 <tests>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
192 <!-- test 1 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
193 <test expect_num_outputs="2">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
194 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
195 <output name="output_summary" file="output_summary.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
196 <output name="output_global_dist" file="output_distribution.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
197 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
198 <!-- test 2 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
199 <test expect_num_outputs="3">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
200 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
201 <param name="per_base_coverage" value="True" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
202 <output name="output_per_base_depth" file="output_per_base_depth.bed" ftype="bedgraph" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
203 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
204 <!-- test 3 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
205 <test expect_num_outputs="4">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
206 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
207 <conditional name="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
208 <param name="window_mode" value="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
209 <param name="region_file" value="input_regions.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
210 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
211 <output name="output_region_dist" file="output_region_distribution_bed.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
212 <output name="output_summary" file="output_region_summary.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
213 <output name="output_regions_bed" file="output_region_depths.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
214 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
215 <!-- test 4 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
216 <test expect_num_outputs="4 ">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
217 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
218 <conditional name="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
219 <param name="window_mode" value="window" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
220 <param name="window_size" value="200" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
221 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
222 <output name="output_region_dist" file="output_region_distribution.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
223 <output name="output_summary" file="output_region_summary_windowed.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
224 <output name="output_regions_bed" file="output_window_depths.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
225 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
226 <!-- test 5 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
227 <test expect_num_outputs="4">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
228 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
229 <conditional name="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
230 <param name="window_mode" value="window" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
231 <param name="window_size" value="200" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
232 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
233 <conditional name="advanced">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
234 <param name="options" value="yes" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
235 <param name="use_median" value="yes" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
236 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
237 <output name="output_region_dist" file="output_region_distribution_median.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
238 <output name="output_summary" file="output_region_summary_windowed_median.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
239 <output name="output_regions_bed" file="output_window_depths_median.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
240 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
241 <!-- test 6 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
242 <test expect_num_outputs="3">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
243 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
244 <conditional name="advanced">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
245 <param name="options" value="yes" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
246 <repeat name="quantize">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
247 <param name="quant_group_mindepth" value="0" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
248 <param name="quant_group_name" value="NO_COVERAGE" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
249 </repeat>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
250 <repeat name="quantize">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
251 <param name="quant_group_mindepth" value="1" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
252 <param name="quant_group_name" value="LOW_COVERAGE" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
253 </repeat>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
254 <repeat name="quantize">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
255 <param name="quant_group_mindepth" value="20" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
256 <param name="quant_group_name" value="SUFFICIENT_COVERAGE" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
257 </repeat>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
258 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
259 <output name="output_quantized_bed" file="output_quantized.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
260 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
261 <!-- test 7 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
262 <test expect_num_outputs="5">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
263 <param name="input_alignment" value="input.bam" ftype="bam" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
264 <conditional name="window">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
265 <param name="window_mode" value="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
266 <param name="region_file" value="input_regions.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
267 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
268 <conditional name="advanced">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
269 <param name="options" value="yes" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
270 <param name="thresholds" value="20,40" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
271 </conditional>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
272 <output name="output_thresholds_bed" file="output_thresholds.bed" ftype="bed" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
273 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
274 <!-- test 7 -->
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
275 <test expect_num_outputs="2">
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
276 <param name="input_alignment" value="input.cram" ftype="cram" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
277 <output name="output_summary" file="output_summary.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
278 <output name="output_global_dist" file="output_distribution.tabular" ftype="tabular" />
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
279 </test>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
280 </tests>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
281 <help><![CDATA[
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
282 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files.
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
283
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
284 It can compute:
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
285
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
286 * mean (or median) depth in fixed-sized windows
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
287 * mean (or median) depth in regions specified by a BED file
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
288 * per base depths
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
289 * a histogram of read depths
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
290 * the mean or median coverage histogram for windows / regions
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
291 * a distribution of proportion of based covered over a particular threshold
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
292 * a BED format report on regions that are defined by coverage thresholds
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
293
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
294 By default, only a summary and depth histogram is computed, but the other options mentioned above can
0
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
295 be enabled using different options in the "Compute depth by region" selector and some of the Advanced
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
296 options.
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
297
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
298 .. _mosdepth: https://github.com/brentp/mosdepth
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
299 ]]></help>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
300 <citations>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
301 <citation type="doi">10.1093/bioinformatics/btx699</citation>
b08cd2e5e61a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit e1c7e5f10bb679ae9987bb63aece4b8b006d3b76
iuc
parents:
diff changeset
302 </citations>
1
a387f00796c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
iuc
parents: 0
diff changeset
303 </tool>