Mercurial > repos > iuc > filtlong
comparison filtlong.xml @ 2:a72af9de6bf5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
author | iuc |
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date | Wed, 31 Mar 2021 08:19:02 +0000 |
parents | 8880fb74ef56 |
children | 41b2ad601cf0 |
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1:8880fb74ef56 | 2:a72af9de6bf5 |
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1 <tool id="filtlong" name="filtlong" version="0.2.0"> | 1 <tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@"> |
2 <description>Filtering long reads by quality</description> | 2 <description>Filtering long reads by quality</description> |
3 <requirements> | 3 <macros> |
4 <requirement type="package" version="0.2.0">filtlong</requirement> | 4 <import>macros.xml</import> |
5 </requirements> | 5 </macros> |
6 <expand macro="requirements"/> | |
6 <version_command>filtlong --version</version_command> | 7 <version_command>filtlong --version</version_command> |
7 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
8 filtlong | 9 filtlong |
9 #if $output_thresholds.target_bases: | 10 #if $output_thresholds.target_bases: |
10 --target_bases '$output_thresholds.target_bases' | 11 --target_bases '$output_thresholds.target_bases' |
41 --window_size '$other.window_size' | 42 --window_size '$other.window_size' |
42 #end if | 43 #end if |
43 '$input_file' > output.fastq | 44 '$input_file' > output.fastq |
44 ]]></command> | 45 ]]></command> |
45 <inputs> | 46 <inputs> |
46 <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/> | 47 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/> |
47 <section name="output_thresholds" title="Output thresholds"> | 48 <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="--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="--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_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_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 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> |
53 </section> | 54 </section> |
54 <section name="external_references" title="External references"> | 55 <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="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/> |
56 <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> | 57 <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> |
57 <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> | 58 <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> |
58 </section> | 59 </section> |
59 <section name="score_weights" title="Score weights"> | 60 <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="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/> |
72 <outputs> | 73 <outputs> |
73 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> | 74 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> |
74 </outputs> | 75 </outputs> |
75 <tests> | 76 <tests> |
76 <test> | 77 <test> |
77 <param name="input_file" ftype="fastqsanger" value="test.fastq"/> | 78 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> |
78 <param name="min_length" value="1000"/> | 79 <param name="min_length" value="1000"/> |
79 <param name="keep_percent" value="50"/> | 80 <param name="keep_percent" value="50"/> |
80 <param name="target_bases" value="500000000"/> | 81 <param name="target_bases" value="500000000"/> |
81 <output name="outfile" ftype="fastqsanger" file="output.fastq"/> | 82 <output name="outfile" ftype="fastqsanger" file="output.fastq"/> |
82 </test> | 83 </test> |
83 <test> | 84 <test> |
84 <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/> | 85 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> |
86 <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/> | |
85 <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/> | 87 <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/> |
86 <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/> | 88 <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/> |
87 <param name="min_length" value="1000"/> | 89 <param name="min_length" value="1000"/> |
88 <param name="keep_percent" value="90"/> | 90 <param name="keep_percent" value="90"/> |
89 <param name="target_bases" value="500000000"/> | 91 <param name="target_bases" value="500000000"/> |