Mercurial > repos > iuc > artic_guppyplex
comparison artic_guppyplex.xml @ 2:372def2f8fd6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
author | iuc |
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date | Mon, 31 Jan 2022 10:12:54 +0000 |
parents | 5ceeb5a5d70f |
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1:5ceeb5a5d70f | 2:372def2f8fd6 |
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1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy1" profile="20.09"> | 1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy2" profile="20.09"> |
2 <description>Filter Nanopore reads by read length and (optionally) quality</description> | 2 <description>Filter Nanopore reads by read length and (optionally) quality</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement> | 7 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement> |
8 </requirements> | 8 </requirements> |
9 <command detect_errors="exit_code"> | 9 <command detect_errors="exit_code"> |
10 <![CDATA[ | 10 <![CDATA[ |
11 mkdir inputs && | 11 mkdir inputs && |
12 #for $i, $elem in enumerate($input) | 12 |
13 ln -fs '$elem' inputs/fastq${i}.fastq && | 13 ## Note about compression handling in the following: |
14 #end for | 14 ## guppyplex use mimetypes.guess_type to guess compression so |
15 ## it's important to get the suffix of the inputs right. | |
16 ## Even if it detects compressed input, it will write uncompressed | |
17 ## output so we need to handle output compression separately. | |
18 | |
19 ## symlink input files to appropriate names in the inputs/ directory | |
20 bash prepare_inputs.sh && | |
21 #if str($input.structure) == 'one_to_one': | |
22 #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz") | |
23 #else: | |
24 #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz") | |
25 #end if | |
15 artic guppyplex --min-length $min_length --max-length $max_length | 26 artic guppyplex --min-length $min_length --max-length $max_length |
27 #if $min_quality == 0: | |
28 --skip-quality-check | |
29 #else: | |
30 --quality $min_quality | |
31 #end if | |
16 --directory inputs/ | 32 --directory inputs/ |
17 --prefix artic_guppyplex --output '$output1' | 33 --output guppyplex_out.fastq |
34 #if $compressed: | |
35 && gzip guppyplex_out.fastq | |
36 #end if | |
18 ]]> | 37 ]]> |
19 </command> | 38 </command> |
39 <configfiles> | |
40 <configfile filename="prepare_inputs.sh"><![CDATA[ | |
41 #if str($input.structure) == 'one_to_one': | |
42 ln -s '$input.reads' inputs/1.${input.reads.ext} | |
43 #else: | |
44 #for $i, $elem in enumerate($input.reads): | |
45 ln -s '$elem' inputs/${i}.${elem.ext} && | |
46 #end for | |
47 : | |
48 #end if | |
49 ]]> | |
50 </configfile> | |
51 </configfiles> | |
20 <inputs> | 52 <inputs> |
21 <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" /> | 53 <conditional name="input"> |
54 <param name="structure" type="select" | |
55 label="Structure of your input data" | |
56 help=""> | |
57 <option value="one_to_one">One input dataset per sample</option> | |
58 <option value="one_to_many">Multiple input datasets per sample</option> | |
59 </param> | |
60 <when value="one_to_one"> | |
61 <param name="reads" type="data" format="@FASTQ_FORMATS@" | |
62 label="Sequencing dataset(s) - one per sample" /> | |
63 </when> | |
64 <when value="one_to_many"> | |
65 <param name="reads" multiple="true" type="data" format="@FASTQ_FORMATS@" | |
66 label="Partial sequencing datasets for your sample" | |
67 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." /> | |
68 </when> | |
69 </conditional> | |
22 <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" /> | 70 <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" /> |
23 <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> | 71 <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> |
24 <param name="skip_quality_check" argument="--skip-quality-check" type="boolean" truevalue="--skip-quality-check" falsevalue="" checked="False" label="Do not filter on quality score (speeds up processing)" /> | 72 <param name="min_quality" type="integer" min="0" value="7" |
73 label="Eliminate reads with a mean base quality score of less than" | |
74 help="Set to 0 to skip the quality check." /> | |
25 </inputs> | 75 </inputs> |
26 <outputs> | 76 <outputs> |
27 <data name="output1" format="fastq" from_work_dir="run_name_.fastq" /> | 77 <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" /> |
28 </outputs> | 78 </outputs> |
29 <tests> | 79 <tests> |
30 <test> | 80 <test> |
31 <param name="input" value="test.fastq" /> | 81 <conditional name="input"> |
32 <output name="output1" file="gupplyplex_output.fastq"/> | 82 <param name="structure" value="one_to_one" /> |
83 <param name="reads" value="test.fastq" /> | |
84 </conditional> | |
85 <output name="output" file="gupplyplex_output.fastq"/> | |
86 </test> | |
87 <test> | |
88 <conditional name="input"> | |
89 <param name="structure" value="one_to_many" /> | |
90 <param name="reads" value="test.fastq,test.fastq" /> | |
91 </conditional> | |
92 <!-- guppyplex drops duplicate reads so we don't need a new | |
93 test file for checking this branch --> | |
94 <output name="output" file="gupplyplex_output.fastq"/> | |
33 </test> | 95 </test> |
34 </tests> | 96 </tests> |
35 <help><![CDATA[ | 97 <help><![CDATA[ |
36 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality. | 98 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality. |
37 This filter is typically used as a pre-processing step in the processing | 99 This filter is typically used as a pre-processing step in the processing |
42 are based on the ARTIC amplicon scheme. If used with a different amplicon | 104 are based on the ARTIC amplicon scheme. If used with a different amplicon |
43 scheme they should be adjusted to use the minimum length of an amplicon as | 105 scheme they should be adjusted to use the minimum length of an amplicon as |
44 the minimum length and the maximum length of an amplicon plus 200 as the | 106 the minimum length and the maximum length of an amplicon plus 200 as the |
45 maximum length. | 107 maximum length. |
46 | 108 |
109 The tool can also be used simultaneously to gather partial fastq | |
110 datasets into single datasets per sample. | |
111 | |
47 .. _ARTIC: https://artic.readthedocs.io/en/latest/ | 112 .. _ARTIC: https://artic.readthedocs.io/en/latest/ |
48 ]]></help> | 113 ]]></help> |
49 <expand macro="citations" /> | 114 <expand macro="citations" /> |
50 </tool> | 115 </tool> |