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comparison porechop.xml @ 3:543cbeef3949 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 6ea6e816d7c92599628ab3c0a0826fb7476270b0"
author iuc
date Thu, 24 Feb 2022 20:08:33 +0000
parents 5f76b20953e5
children
comparison
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2:5f76b20953e5 3:543cbeef3949
1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@" profile="20.01"> 1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@+galaxy0" profile="20.01">
2 <description>adapter trimmer for Oxford Nanopore reads</description> 2 <description>adapter trimmer for Oxford Nanopore reads</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">0.2.4</token> 4 <token name="@WRAPPER_VERSION@">0.2.4</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
30 --min_split_read_size '$middle_adapter_settings.min_split_read_size' 30 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
31 -o 'out.$format' 31 -o 'out.$format'
32 32
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" /> 35 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
36 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads"> 36 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads">
37 <option selected="True" value="fasta">fasta</option> 37 <option selected="True" value="fasta">fasta</option>
38 <option value="fastq">fastq</option> 38 <option value="fastq">fastq</option>
39 <option value="fasta.gz">fasta.gz</option> 39 <option value="fasta.gz">fasta.gz</option>
40 <option value="fastq.gz">fastq.gz</option> 40 <option value="fastq.gz">fastq.gz</option>
103 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/> 103 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/>
104 <param name="format" value="fastq"/> 104 <param name="format" value="fastq"/>
105 <output name="outfile" ftype="fastqsanger" file="out.fastq"/> 105 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
106 </test> 106 </test>
107 <test> 107 <test>
108 <param name="input_file" ftype="fastq.gz" value="test_format.fastq.gz"/>
109 <param name="format" value="fastq"/>
110 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
111 </test>
112 <test>
108 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 113 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
109 <param name="format" value="fasta.gz"/> 114 <param name="format" value="fasta.gz"/>
110 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/> 115 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/>
111 </test> 116 </test>
112 <test> 117 <test>