comparison make_decoy.xml @ 0:a929e27eb203 draft

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author iracooke
date Thu, 21 Jun 2012 22:30:48 -0400
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1 <tool id="make_decoy_1" name="Create decoy databases" version="1.0.0">
2 <requirements>
3 <requirement type="package">protk</requirement>
4 </requirements>
5
6 <description>Creates a random protein database with similar properties to a real protein database</description>
7
8 <command>make_decoy.rb $input_file -o $output -L $length -P $prefix $append</command>
9
10 <inputs>
11
12 <param name="input_file" type="data" format="fasta" multiple="false" label="Input File" help="Real protein sequences. Take care that these are fasta formatted with no more than 80 amino acids per line. There should be no whitespace in the sequences."/>
13 <param name="prefix" type="text" label="String to prepend to generated protein ID's" size="60" value="decoy_"/>
14 <param name="length" type="text" label="Number of random sequences to generate" help="If 0, a database of equal size to the input database will be generated" size="60" value="0"/>
15 <param name="append" type="boolean" checked="true" label="Append input dataset to the generated sequences" truevalue="-A" falsevalue=""/>
16 </inputs>
17
18 <outputs>
19 <data format="fasta" name="output" metadata_source="input_file" label="Random sequences from ${input_file.display_name}" from_work_dir="random.fasta"/>
20 </outputs>
21
22 <help>
23 Create random protein sequences
24 </help>
25
26 </tool>