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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong commit 5875d08292df3ceac45962dcc1790a36de9dcf9a
author iuc
date Tue, 23 Sep 2025 16:33:00 +0000
parents e6d48d485920
children
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3:e6d48d485920 4:428fd2cee5d9
1 <tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Filtering long reads by quality</description> 2 <description>Filtering long reads by quality</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools" />
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <version_command>filtlong --version</version_command> 8 <version_command>filtlong --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 filtlong 10 filtlong
10 #if $output_thresholds.target_bases: 11 #if $output_thresholds.target_bases:
26 --max_length '$output_thresholds.max_length' 27 --max_length '$output_thresholds.max_length'
27 #end if 28 #end if
28 #if $external_references.assembly: 29 #if $external_references.assembly:
29 --assembly '$external_references.assembly' 30 --assembly '$external_references.assembly'
30 #end if 31 #end if
31 #if $external_references.illumina_1: 32 #if $external_references.short_1:
32 --illumina_1 '$external_references.illumina_1' 33 --short_1 '$external_references.short_1'
33 #end if 34 #end if
34 #if $external_references.illumina_2: 35 #if $external_references.short_2:
35 --illumina_2 '$external_references.illumina_2' 36 --short_2 '$external_references.short_2'
36 #end if 37 #end if
37 --length_weight '$score_weights.length_weight' 38 --length_weight '$score_weights.length_weight'
38 --mean_q_weight '$score_weights.mean_q_weight' 39 --mean_q_weight '$score_weights.mean_q_weight'
39 --window_q_weight '$score_weights.window_q_weight' 40 --window_q_weight '$score_weights.window_q_weight'
40 $read_manipulation.trim 41 $read_manipulation.trim
47 '$input_file' > output.fastq 48 '$input_file' > output.fastq
48 ]]></command> 49 ]]></command>
49 <inputs> 50 <inputs>
50 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/> 51 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
51 <section name="output_thresholds" title="Output thresholds"> 52 <section name="output_thresholds" title="Output thresholds">
52 <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> 53 <param argument="--target_bases" type="text" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases (unit suffixes: k, kb, m, mb, g, gb).">
54 <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
55 </param>
53 <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> 56 <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
54 <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/> 57 <param argument="--max_length" type="text" min="0" optional="True" label="Max. length" help="Maximum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
55 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/> 58 <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
59 </param>
60 <param argument="--min_length" type="text" min="0" optional="True" label="Min. length" help="Minimum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
61 <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
62 </param>
56 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/> 63 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
57 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> 64 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
58 </section> 65 </section>
59 <section name="external_references" title="External references"> 66 <section name="external_references" title="External references">
60 <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/> 67 <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
61 <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> 68 <param argument="--short_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
62 <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> 69 <param argument="--short_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
63 </section> 70 </section>
64 <section name="score_weights" title="Score weights"> 71 <section name="score_weights" title="Score weights">
65 <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/> 72 <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
66 <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/> 73 <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
67 <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/> 74 <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>
68 </section> 75 </section>
69 <section name="read_manipulation" title="Read manipulation"> 76 <section name="read_manipulation" title="Read manipulation">
70 <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/> 77 <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
71 <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/> 78 <param argument="--split" type="text" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases">
79 <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
80 </param>
72 </section> 81 </section>
73 <section name="other" title="Other"> 82 <section name="other" title="Other">
74 <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/> 83 <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
75 </section> 84 </section>
76 </inputs> 85 </inputs>
77 <outputs> 86 <outputs>
78 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> 87 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
79 </outputs> 88 </outputs>
80 <tests> 89 <tests>
81 <test> 90 <test expect_num_outputs="1">
82 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> 91 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
83 <param name="min_length" value="1000"/> 92 <section name="output_thresholds">
84 <param name="keep_percent" value="50"/> 93 <param name="min_length" value="1000"/>
85 <param name="target_bases" value="500000000"/> 94 <param name="keep_percent" value="50"/>
95 <param name="target_bases" value="500mb"/>
96 </section>
86 <output name="outfile" ftype="fastqsanger" file="output.fastq"/> 97 <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
87 </test> 98 </test>
88 <test> 99 <test expect_num_outputs="1">
89 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> 100 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
90 <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/> 101 <section name="external_references">
91 <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/> 102 <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
92 <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/> 103 <param name="short_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
93 <param name="min_length" value="1000"/> 104 <param name="short_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
94 <param name="keep_percent" value="90"/> 105 </section>
95 <param name="target_bases" value="500000000"/> 106 <section name="output_thresholds">
96 <param name="trim" value="True"/> 107 <param name="min_length" value="1000"/>
97 <param name="split" value="500"/> 108 <param name="keep_percent" value="90"/>
109 <param name="target_bases" value="500mb"/>
110 </section>
111 <section name="read_manipulation">
112 <param name="trim" value="True"/>
113 <param name="split" value="500"/>
114 </section>
98 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/> 115 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
99 </test> 116 </test>
100 <test> 117 <test expect_num_outputs="1">
101 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> 118 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
102 <param name="max_length" value="5000"/> 119 <section name="output_thresholds">
120 <param name="max_length" value="5000"/>
121 </section>
103 <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/> 122 <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
104 </test> 123 </test>
105 </tests> 124 </tests>
106 <help><![CDATA[ 125 <help><![CDATA[
107 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 126 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
108 ]]></help> 127 ]]></help>
109 <citations> 128 <expand macro="citations"/>
110 <citation type="bibtex">
111 @misc{rrwick2017,
112 author = {Wick, Ryan},
113 year = {2017},
114 title = {Filtlong},
115 publisher = {GitHub},
116 journal = {GitHub repository},
117 url = {https://github.com/rrwick/Filtlong},
118 }
119 </citation>
120 </citations>
121 </tool> 129 </tool>