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