Mercurial > repos > iuc > artic_guppyplex

annotate artic_guppyplex.xml @ 5:311d11c4a68b 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/artic commit 9fe39fd1ad0c1a5af9e8d2d633fd3e7404adbac7
author iuc
date Mon, 24 Feb 2025 13:54:49 +0000
parents 76d6358f71b7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@TOOL_VERSION@+galaxy0" profile="20.09">
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
2 <description>Filter Nanopore reads by read length and (optionally) quality</description>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
3 <macros>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
5 </macros>
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
6 <expand macro="requirements"/>
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
8 <![CDATA[
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
9 mkdir inputs &&
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
10
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
11 ## Note about compression handling in the following:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
12 ## guppyplex use mimetypes.guess_type to guess compression so
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
13 ## it's important to get the suffix of the inputs right.
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
14 ## Even if it detects compressed input, it will write uncompressed
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
15 ## output so we need to handle output compression separately.
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
16
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
17 ## symlink input files to appropriate names in the inputs/ directory
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
18 bash prepare_inputs.sh &&
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
19 #if str($input.structure) == 'one_to_one':
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
20 #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz")
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
21 #else:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
22 #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz")
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
23 #end if
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
24
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
25 artic guppyplex
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
26 --min-length $min_length
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
27 --max-length $max_length
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
28 #if $min_quality == 0:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
29 --skip-quality-check
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
30 #else:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
31 --quality $min_quality
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
32 #end if
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
33 --directory inputs/
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
34 --output guppyplex_out.fastq
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
35 #if $compressed:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
36 && gzip guppyplex_out.fastq
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
37 #end if
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
38 ]]>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
39 </command>
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
40 <configfiles>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
41 <configfile filename="prepare_inputs.sh"><![CDATA[
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
42 #if str($input.structure) == 'one_to_one':
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
43 ln -s '$input.reads' inputs/1.${input.reads.ext}
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
44 #else:
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
45 #for $i, $elem in enumerate($input.reads):
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
46 ln -s '$elem' inputs/${i}.${elem.ext} &&
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
47 #end for
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
48 :
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
49 #end if
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
50 ]]>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
51 </configfile>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
52 </configfiles>
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
53 <inputs>
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
54 <conditional name="input">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
55 <param name="structure" type="select"
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
56 label="Structure of your input data"
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
57 help="">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
58 <option value="one_to_one">One input dataset per sample</option>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
59 <option value="one_to_many">Multiple input datasets per sample</option>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
60 </param>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
61 <when value="one_to_one">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
62 <param name="reads" type="data" format="@FASTQ_FORMATS@"
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
63 label="Sequencing dataset(s) - one per sample" />
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
64 </when>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
65 <when value="one_to_many">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
66 <param name="reads" multiple="true" type="data" format="@FASTQ_FORMATS@"
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
67 label="Partial sequencing datasets for your sample"
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
68 help="Multiple datasets selected here will get combined into a single output for a single assumed sample. Select a nested list to have its inner lists interpreted as data from one sample each and to obtain one output per inner list." />
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
69 </when>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
70 </conditional>
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
71 <param name="max_length" type="integer" value="700" min="1" label="Maximum read length" help="Remove reads greater than this number of base pairs" />
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
72 <param name="min_length" type="integer" value="400" min="1" label="Minimum read length" help="Remove reads less than this number of base pairs" />
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
73 <param name="min_quality"
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
74 optional="true" type="integer" min="0" value="7"
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
75 label="Minimum read quality"
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
76 help="Remove reads with average quality lower than this number. Set to 0 to skip the quality check." />
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
77 </inputs>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
78 <outputs>
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
79 <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" />
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
80 </outputs>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
81 <tests>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
82 <test>
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
83 <conditional name="input">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
84 <param name="structure" value="one_to_one" />
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
85 <param name="reads" value="test.fastq.gz" />
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
86 </conditional>
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
87 <output name="output">
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
88 <assert_contents>
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
89 <has_size value="72300" delta="1000" />
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
90 </assert_contents>
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
91 </output>
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
92 </test>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
93 <test>
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
94 <conditional name="input">
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
95 <param name="structure" value="one_to_many" />
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
96 <param name="reads" value="test.fastq.gz,test.fastq.gz" />
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
97 </conditional>
4
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
98 <output name="output">
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
99 <assert_contents>
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
100 <has_size value="72300" delta="200" />
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
101 </assert_contents>
76d6358f71b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e
iuc
parents: 2
diff changeset
102 </output>
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
103 </test>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
104 </tests>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
105 <help><![CDATA[
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
106 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality.
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
107 This filter is typically used as a pre-processing step in the processing
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
108 of amplicon sequencing Nanopore reads, where a size-based filter can
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
109 be used to remove possibly-chimeric reads.
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
110
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
111 The default paramters of the tool (minimum length of 400 and maximum of 700)
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
112 are based on the ARTIC amplicon scheme. If used with a different amplicon
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
113 scheme they should be adjusted to use the minimum length of an amplicon as
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
114 the minimum length and the maximum length of an amplicon plus 200 as the
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
115 maximum length.
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
116
2
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
117 The tool can also be used simultaneously to gather partial fastq
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
118 datasets into single datasets per sample.
372def2f8fd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
iuc
parents: 1
diff changeset
119
0
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
120 .. _ARTIC: https://artic.readthedocs.io/en/latest/
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
121 ]]></help>
7a82006f7c05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
122 <expand macro="citations" />
1
5ceeb5a5d70f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"
iuc
parents: 0
diff changeset
123 </tool>