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comparison porechop.xml @ 1:93d623d9979c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
author iuc
date Wed, 19 Sep 2018 08:35:02 -0400
parents 24822689acf8
children 5f76b20953e5
comparison
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0:24822689acf8 1:93d623d9979c
27 --min_split_read_size '$middle_adapter_settings.min_split_read_size' 27 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
28 -o 'out.$format' 28 -o 'out.$format'
29 29
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="input_file" type="data" format="fasta,fastq" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" /> 32 <param name="input_file" type="data" format="fasta,fastqsanger" 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 - if auto, the format will be chosen based on the output filename or the input read format"> 33 <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> 34 <option selected="True" value="fasta">fasta</option>
35 <option value="fastq">FASTQ</option> 35 <option value="fastq">fastq</option>
36 <option value="fasta.gz">FASTA.gz</option> 36 <option value="fasta.gz">fasta.gz</option>
37 <option value="fastq.gz">FASTQ.gz</option> 37 <option value="fastq.gz">fastq.gz</option>
38 </param> 38 </param>
39 <section name="barcode_binning_settings" title="Barcode binning settings"> 39 <section name="barcode_binning_settings" title="Barcode binning settings">
40 <param argument="--barcode_threshold" type="float" min="0" max="100" value="75.0" optional="True" label="Percent identity for binning" 40 <param argument="--barcode_threshold" type="float" min="0" max="100" value="75.0" optional="True" label="Percent identity for binning"
41 help="A read must have at least this percent identity to a barcode to be binned (default: 75.0)"/> 41 help="A read must have at least this percent identity to a barcode to be binned (default: 75.0)"/>
42 <param argument="--barcode_diff" type="float" min="0" max="100" value="5.0" optional="True" label="Minimum difference in identity" 42 <param argument="--barcode_diff" type="float" min="0" max="100" value="5.0" optional="True" label="Minimum difference in identity"
82 </section> 82 </section>
83 </inputs> 83 </inputs>
84 <outputs> 84 <outputs>
85 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed"> 85 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed">
86 <change_format> 86 <change_format>
87 <when input="format" value="fastq" format="fastq"/> 87 <when input="format" value="fastq" format="fastqsanger"/>
88 <when input="format" value="fasta.gz" format="fasta.gz"/> 88 <when input="format" value="fasta.gz" format="fasta.gz"/>
89 <when input="format" value="fastq.gz" format="fastq.gz"/> 89 <when input="format" value="fastq.gz" format="fastqsanger.gz"/>
90 </change_format> 90 </change_format>
91 </data> 91 </data>
92 </outputs> 92 </outputs>
93 <tests> 93 <tests>
94 <test> 94 <test>
97 <output name="outfile" ftype="fasta" file="out.fasta"/> 97 <output name="outfile" ftype="fasta" file="out.fasta"/>
98 </test> 98 </test>
99 <test> 99 <test>
100 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 100 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
101 <param name="format" value="fastq"/> 101 <param name="format" value="fastq"/>
102 <output name="outfile" ftype="fastq" file="out.fastq"/> 102 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
103 </test> 103 </test>
104 <test> 104 <test>
105 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 105 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
106 <param name="format" value="fasta.gz"/> 106 <param name="format" value="fasta.gz"/>
107 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/> 107 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/>
108 </test> 108 </test>
109 <test> 109 <test>
110 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 110 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
111 <param name="format" value="fastq.gz"/> 111 <param name="format" value="fastq.gz"/>
112 <output name="outfile" ftype="fastq.gz" file="out.fastq.gz" compare="sim_size"/> 112 <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/>
113 </test> 113 </test>
114 <test> 114 <test>
115 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 115 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
116 <param name="format" value="fasta"/> 116 <param name="format" value="fasta"/>
117 <param name="barcode_threshold" value="70"/> 117 <param name="barcode_threshold" value="70"/>