Mercurial > repos > nedias > orf_tools
comparison orf_tool.xml @ 4:04de7d352a3d draft
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| author | nedias |
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| date | Wed, 12 Oct 2016 00:04:57 -0400 |
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| 3:0095bf758b19 | 4:04de7d352a3d |
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| 1 <tool id="orf_tool" name="Open Reading Frame Extract Tool" version="0.1.0"> | |
| 2 <description>from given fasta RNA sequence</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.64">biopython</requirement> | |
| 5 <requirement type="python-module">Bio</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <!-- Anything other than zero is an error --> | |
| 9 <exit_code range="1:" /> | |
| 10 <exit_code range=":-1" /> | |
| 11 </stdio> | |
| 12 <version_command interpreter="python">entry.py --version</version_command> | |
| 13 <command interpreter="python"> | |
| 14 entry.py -i "$input_file" -a "$output_all" -d "$output_dest" -f "$ext" -l "$length" | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." /> | |
| 18 <param name="ext" type="select" value="fasta" label="Input file type"> | |
| 19 <option value="fasta">Fasta</option> | |
| 20 <option value="fastq">Fastq</option> | |
| 21 <option value="sam">Sam</option> | |
| 22 <option value="bam">Bam</option> | |
| 23 </param> | |
| 24 <param name="length" type="integer" value="100" max="100" min="1" label="Length" help="Percentage of the max match." /> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data name="output_all" format_source="input_file" metadata_source="input_file" label="$input_file.name all matches"> | |
| 28 </data> | |
| 29 <data name="output_dest" format_source="input_file" metadata_source="input_file" label="$input_file.name designated matches"> | |
| 30 </data> | |
| 31 </outputs> | |
| 32 </tool> |