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comparison make_decoy.xml @ 0:45dee11aa2bf draft

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author iracooke
date Tue, 18 Mar 2014 20:50:51 -0400
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1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.2.6">protk</requirement>
4 </requirements>
5
6 <description>Generate random protein sequences with the same AA composition and input sequences</description>
7
8 <command>
9 make_decoy.rb $fasta_file -o $output
10 -P $prefix_string
11 $append
12
13 </command>
14
15
16
17
18 <stdio>
19 <exit_code range="1:" level="fatal" description="Failure" />
20 </stdio>
21
22 <inputs>
23 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
24 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
25 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
26 </inputs>
27
28 <outputs>
29 <data format="fasta" name="output" />
30 </outputs>
31
32
33 <help>
34
35 **What it does**
36
37 Generates random protein sequences based on a given set of input sequences. To be used for decoy proteomics searches
38
39 ----
40
41 **References**
42
43
44 </help>
45
46 </tool>