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comparison filtlong.xml @ 0:f7c6dcf60964 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
author iuc
date Mon, 17 Sep 2018 16:15:35 -0400
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children 33efcf418297
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-1:000000000000 0:f7c6dcf60964
1 <tool id="filtlong" name="filtlong" version="0.2.0">
2 <description>Filtering long reads by quality</description>
3 <requirements>
4 <requirement type="package" version="0.2.0">filtlong</requirement>
5 </requirements>
6 <version_command>filtlong --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[
8 filtlong
9 #if $output_thresholds.target_bases:
10 --target_bases '$output_thresholds.target_bases'
11 #end if
12 #if $output_thresholds.keep_percent:
13 --keep_percent '$output_thresholds.keep_percent'
14 #end if
15 #if $output_thresholds.min_length:
16 --min_length '$output_thresholds.min_length'
17 #end if
18 #if $output_thresholds.min_mean_q:
19 --min_mean_q '$output_thresholds.min_mean_q'
20 #end if
21 #if $output_thresholds.min_window_q:
22 --min_window_q '$output_thresholds.min_window_q'
23 #end if
24 #if $external_references.assembly:
25 --assembly '$external_references.assembly'
26 #end if
27 #if $external_references.illumina_1:
28 --illumina_1 '$external_references.illumina_1'
29 #end if
30 #if $external_references.illumina_2:
31 --illumina_2 '$external_references.illumina_2'
32 #end if
33 --length_weight '$score_weights.length_weight'
34 --mean_q_weight '$score_weights.mean_q_weight'
35 --window_q_weight '$score_weights.window_q_weight'
36 $read_manipulation.trim
37 #if $read_manipulation.split:
38 --split '$read_manipulation.split'
39 #end if
40 #if $other.window_size:
41 --window_size '$other.window_size'
42 #end if
43 '$input_file' > output.fastq
44 ]]></command>
45 <inputs>
46 <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/>
47 <section name="output_thresholds" title="Output thresholds">
48 <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"/>
49 <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)"/>
50 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
51 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
52 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
53 </section>
54 <section name="external_references" title="External references">
55 <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
56 <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
57 <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
58 </section>
59 <section name="score_weights" title="Score weights">
60 <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)"/>
61 <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)"/>
62 <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)"/>
63 </section>
64 <section name="read_manipulation" title="Read manipulation">
65 <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"/>
66 <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"/>
67 </section>
68 <section name="other" title="Other">
69 <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)"/>
70 </section>
71 </inputs>
72 <outputs>
73 <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
74 </outputs>
75 <tests>
76 <test>
77 <param name="input_file" ftype="fastq" value="test.fastq"/>
78 <param name="min_length" value="1000"/>
79 <param name="keep_percent" value="50"/>
80 <param name="target_bases" value="500000000"/>
81 <output name="outfile" ftype="fastq" file="output.fastq"/>
82 </test>
83 <test>
84 <param name="input_file" ftype="fastq" value="test_reference.fasta"/>
85 <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/>
86 <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/>
87 <param name="min_length" value="1000"/>
88 <param name="keep_percent" value="90"/>
89 <param name="target_bases" value="500000000"/>
90 <param name="trim" value="True"/>
91 <param name="split" value="500"/>
92 <output name="outfile" ftype="fastq" file="output_reference.fastq"/>
93 </test>
94 </tests>
95 <help><![CDATA[
96 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.
97 ]]></help>
98 <citations>
99 <citation type="bibtex">
100 @misc{rrwick2017,
101 author = {Wick, Ryan},
102 year = {2017},
103 title = {Filtlong},
104 publisher = {GitHub},
105 journal = {GitHub repository},
106 url = {https://github.com/rrwick/Filtlong},
107 }
108 </citation>
109 </citations>
110 </tool>