Mercurial > repos > iuc > porechop

comparison porechop.xml @ 2:5f76b20953e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit e68e5869f08e66fbe2787f23b58c1d66e61d9df2"
author iuc
date Fri, 02 Apr 2021 19:38:37 +0000
parents 93d623d9979c
children 543cbeef3949
comparison
equal deleted inserted replaced
1:93d623d9979c 2:5f76b20953e5
1 <tool id="porechop" name="Porechop" version="0.2.3"> 1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@" profile="20.01">
2 <description>adapter trimmer for Oxford Nanopore reads</description> 2 <description>adapter trimmer for Oxford Nanopore reads</description>
3 <macros>
4 <token name="@WRAPPER_VERSION@">0.2.4</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.2.3_seqan2.1.1">porechop</requirement> 7 <requirement type="package" version="@WRAPPER_VERSION@">porechop</requirement>
5 </requirements> 8 </requirements>
6 <version_command>porechop --version</version_command> 9 <version_command>porechop --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
8 porechop 11 porechop
9 -i '$input_file' 12 -i '$input_file'
27 --min_split_read_size '$middle_adapter_settings.min_split_read_size' 30 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
28 -o 'out.$format' 31 -o 'out.$format'
29 32
30 ]]></command> 33 ]]></command>
31 <inputs> 34 <inputs>
32 <param name="input_file" type="data" format="fasta,fastqsanger" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" /> 35 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
33 <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">
34 <option selected="True" value="fasta">fasta</option> 37 <option selected="True" value="fasta">fasta</option>
35 <option value="fastq">fastq</option> 38 <option value="fastq">fastq</option>
36 <option value="fasta.gz">fasta.gz</option> 39 <option value="fasta.gz">fasta.gz</option>
37 <option value="fastq.gz">fastq.gz</option> 40 <option value="fastq.gz">fastq.gz</option>
95 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 98 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
96 <param name="format" value="fasta"/> 99 <param name="format" value="fasta"/>
97 <output name="outfile" ftype="fasta" file="out.fasta"/> 100 <output name="outfile" ftype="fasta" file="out.fasta"/>
98 </test> 101 </test>
99 <test> 102 <test>
100 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 103 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/>
101 <param name="format" value="fastq"/> 104 <param name="format" value="fastq"/>
102 <output name="outfile" ftype="fastqsanger" file="out.fastq"/> 105 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
103 </test> 106 </test>
104 <test> 107 <test>
105 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 108 <param name="input_file" ftype="fasta" value="test_format.fasta"/>