Mercurial > repos > iuc > ivar_trim

annotate ivar_trim.xml @ 20:6ca0648a3926 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/master/tools/ivar/ commit 249acacf7a562ab99130d311b7e322a80993ca44
author iuc
date Thu, 13 Mar 2025 08:59:26 +0000
parents fc7242e3b97b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
7567f77ffbc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
iuc
parents: 13
diff changeset
1 <tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
2 <description>Trim reads in aligned BAM</description>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
3 <macros>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
5 </macros>
19
fc7242e3b97b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit b548a504e88bd330f534be0dd018175c9341b1f1
iuc
parents: 16
diff changeset
6 <expand macro="xrefs"/>
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
7 <expand macro="requirements"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
8 <expand macro="version_command"/>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
10 #if $primer.source == 'history'
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
11 cp '$primer.input_bed' bed.bed &&
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
12 #else
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
13 cp '$primer.cached_bed.fields.path' bed.bed &&
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
14 #end if
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
15 python '$__tool_directory__/sanitize_bed.py' bed.bed &&
10
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
iuc
parents: 9
diff changeset
16 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
iuc
parents: 9
diff changeset
17 #if $amplicons.filter_by == 'yes_compute':
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
18 python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv &&
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
19 #else
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
20 ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv &&
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
21 #end if
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
22 python '$__tool_directory__/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv &&
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
23 #end if
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
24 ln -s '$input_bam' sorted.bam &&
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
25 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
26
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
27 ivar trim
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
28 -i sorted.bam
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
29 -b bed.bed
13
a15b0f953cf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a16957b7f6cb8687daafb005c0036abebce59b26
iuc
parents: 12
diff changeset
30 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
31 -f amplicon_info.tsv
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
32 #end if
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
33 -x $primer_pos_wiggle
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
34 $inc_primers
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
35 #if $trimmed_length.filter == 'off':
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
36 -m 0
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
37 #elif $trimmed_length.filter == 'auto':
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
38 -m -1
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
39 #else:
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
40 -m $trimmed_length.min_len
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
41 #end if
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
42 -q $min_qual
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
43 -s $window_width
16
5f78c8457b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 51d656555f9635bb8988f9eec904ee66657736e1
iuc
parents: 15
diff changeset
44 | samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam -
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
45 ]]></command>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
46 <inputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
47 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
48 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
49 <param label="Source of primer information" name="source" type="select">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
50 <option value="history" selected="true">History</option>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
51 <option value="cached">Built-in</option>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
52 </param>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
53 <when value="history">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
54 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
55 </when>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
56 <when value="cached">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
57 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
58 <options from_data_table="primer_scheme_bedfiles">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
59 <filter type="sort_by" column="1" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
60 <validator type="no_options" message="No primer schemes are available" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
61 </options>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
62 </param>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
63 </when>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
64 </conditional>
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
65 <conditional name="amplicons">
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
66 <param name="filter_by" type="select"
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
67 label="Filter reads based on amplicon info"
9
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
68 help="When you select Yes, reads that are not fully contained in any amplicon will be dropped before primer trimming. This option is currently marked as [Experimental] in ivar, but nevertheless recommended here. Info on amplicons can be computed from suitable primer BED files (see tool help below) or provided by the user. ">
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
69 <option value="">No, allow reads to extend beyond amplicon boundaries</option>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
70 <option value="yes_compute">Yes, drop reads that extend beyond amplicon boundaries</option>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
71 <option value="yes">Yes, drop reads that extend beyond amplicon boundaries and use my amplicon info file</option>
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
72 </param>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
73 <when value="yes_compute" />
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
74 <when value="yes">
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
75 <param name="amplicon_info" argument="-f" type="data" format="tabular" />
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
76 </when>
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
77 <when value="" />
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
78 </conditional>
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
79 <param name="primer_pos_wiggle" argument="-x" type="integer" min="0" value="0"
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
80 label="Wiggling room for read ends relative to primer binding sites"
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
81 help="Reads that occur at the specified offset positions relative to primer positions (as annotated in the primer information dataset) will also be trimmed (default: 0)" />
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
82 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/>
13
a15b0f953cf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a16957b7f6cb8687daafb005c0036abebce59b26
iuc
parents: 12
diff changeset
83 <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality threshold for sliding window to pass"/>
a15b0f953cf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a16957b7f6cb8687daafb005c0036abebce59b26
iuc
parents: 12
diff changeset
84 <param name="window_width" argument="-s" type="integer" min="0" max="255" value="4" label="Width of sliding window"/>
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
85 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
86 <param name="filter" type="select" label="Require a minimum length for reads to retain them after any trimming?" help="The default automatic setting will determine the threshold as 50% of the mean length of the first 1000 raw input reads, which may or may not be adequate for your data. You can always make the outcome of filtering more predictable by specifying the threshold explicitly. You can also opt to retain reads independently of their trimmed length, but typically this only makes sense if you are performing additional read filtering with additional tools in your analysis pipeline.">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
87 <option value="off">No, keep reads independently of their trimmed length (-m 0)</option>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
88 <option value="auto" selected="true">Yes, and determine required length threshold automatically from input (-m -1)</option>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
89 <option value="custom">Yes, and provide a custom threshold</option>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
90 </param>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
91 <when value="off" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
92 <when value="auto" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
93 <when value="custom">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
94 <param name="min_len" argument="-m" type="integer" min="1" value="30" label="Minimum trimmed length threshold" help="Reads with a trimmed length shorter than this value will be discarded."/>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
95 </when>
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
96 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
97 </inputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
98 <outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
99 <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
100 </outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
101 <tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
102 <!-- #1: SARS-Cov data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
103 <test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
104 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
105 <param name="input_bed" value="covid19/ARTIC-V1.bed" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
106 <param name="inc_primers" value="true" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
107 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
108 <param name="filter" value="custom" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
109 <param name="min_len" value="30" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
110 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
111 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
112 </test>
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
113 <test>
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
114 <!-- Test with primer bed file that needs to be sanitized -->
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
115 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
116 <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" />
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
117 <param name="inc_primers" value="true" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
118 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
119 <param name="filter" value="custom" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
120 <param name="min_len" value="30" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
121 </conditional>
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
122 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
123 </test>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
124 <!-- #1: Zika data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
125 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
126 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
127 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
128 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
129 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
130 <param name="input_bam" value="zika/Z52_a.sorted.bam" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
131 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
132 <param name="filter" value="custom" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
133 <param name="min_len" value="30" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
134 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
135 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
136 </test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
137 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
138 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
139 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
140 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
141 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
142 <param name="input_bam" value="zika/Z52_b.sorted.bam" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
143 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
144 <param name="filter" value="auto" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
145 </conditional>
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
146 <output name="output_bam" ftype="bam">
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
147 <assert_contents>
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
148 <has_size value="3373924" delta="1000"/>
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
149 </assert_contents>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
150 </output>
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
151 <assert_stderr>
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
152 <has_text text="Found 68 primers in BED file"/>
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
153 <has_text text="reads were quality trimmed below the minimum length of 125 bp and were not written to file"/>
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 11
diff changeset
154 <has_text text="reads that started outside of primer regions were not written to file"/>
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
155 </assert_stderr>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
156 </test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
157 <test>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
158 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
159 <param name="source" value="cached" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
160 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
161 </conditional>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
162 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
163 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
164 <param name="filter" value="custom" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
165 <param name="min_len" value="30" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
166 </conditional>
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
167 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
168 </test>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
169 <test>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
170 <conditional name="primer">
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
171 <param name="source" value="cached" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
172 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
173 </conditional>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
174 <conditional name="amplicons">
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
175 <param name="filter_by" value="yes_compute" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
176 </conditional>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
177 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
178 <conditional name="trimmed_length">
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
179 <param name="filter" value="custom" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
180 <param name="min_len" value="30" />
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
181 </conditional>
10
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
iuc
parents: 9
diff changeset
182 <assert_command>
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
iuc
parents: 9
diff changeset
183 <has_text text="write_amplicon_info_file" />
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
iuc
parents: 9
diff changeset
184 </assert_command>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
185 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
186 </test>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
187 </tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
188 <help><![CDATA[
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
189 iVar uses primer positions supplied in a BED file to soft clip primer
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
190 sequences from an aligned and sorted BAM file. Following this, the reads are
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
191 trimmed further based on a quality threshold.
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
192
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
193 **Primer and Amplicon info**
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
194
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
195 The tool requires information about primers and their binding sites in 6-column
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
196 BED format. The information from this file is used to decide whether any mapped
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
197 read in the BAM input ends with a primer sequence and should, thus, be
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
198 soft-clipped.
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
199
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
200 Optionally, the tool can also discard reads that do not fully map to within any
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
201 amplicon. Such reads are likely to be wet-lab or mapping artefacts and removing
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
202 them can increase variant calling precision. To calculate the extent of
9
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
203 expected amplicons the tool needs to know which primers work together to form
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
204 an amplicon. The tool can try to deduce this info from the names of the primers
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
205 found in the primer info dataset. This will require a primer naming scheme
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
206 following the regex pattern::
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
207
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
208 .*_(?P<amplicon_number>\d+).*_(?P<primer_orientation>L(?:EFT)?|R(?:IGHT)?)
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
209
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
210 *i.e.*, the following schemes will work (and get parsed as):
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
211
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
212 - ``nCoV-2019_1_LEFT`` (forward primer of amplicon 1)
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
213
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
214 - ``400_2_out_R`` (reverse primer of amplicon 2)
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
215
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
216 - ``QIAseq_163-2_LEFT`` (forward primer of amplicon 163)
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
217
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
218 Alternatively, you can specify the amplicon information explicitly through a
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
219 dataset that lists the names of primers that together form any given amplicon.
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
220 In it, primer names (exactly matching those in the primer info dataset) need to
6239a4153059 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
iuc
parents: 8
diff changeset
221 be TAB-separated with one line per amplicon.
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
222 If the primer scheme has more than two primers contributing to a given amplicon
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
223 (in schemes using alternate primers), you can (in this Galaxy tool only)
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
224 specify all of them on one line and the tool will calculate the maximum extent
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
225 of the amplicon.
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
226
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
227 **Quality trimming details and final length filtering**
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
228
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
229 To do the quality trimming, iVar uses a sliding window approach. The window
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
230 slides from the 5' end to the 3' end and if at any point the average base
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
231 quality in the window falls below the threshold, the remaining read is soft
15
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
232 clipped.
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
233
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
234 Finally, the trimmed length threshold gets applied if specified, and fully
02eecd020c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
iuc
parents: 14
diff changeset
235 trimmed surviving reads are written to the BAM output.
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
236
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
237 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents: 4
diff changeset
238 ]]></help>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
239 <expand macro="citations" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
240 </tool>