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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:37:19 -0400
parents 354e820eb485
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1:354e820eb485 2:bd4844c664f2
1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0"> 1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1">
2 <requirements> 2 <description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 Generate random protein sequences with the same AA composition as input sequences
4 <requirement type="package" version="1.4">protk</requirement> 4 </description>
5 </requirements> 5 <requirements>
6 6 <container type="docker">iracooke/protk-1.4.3</container>
7 <description> 7 <requirement type="package" version="1.4.3">protk</requirement>
8 Generate random protein sequences with the same AA composition as input sequences 8 </requirements>
9 </description> 9 <stdio>
10 10 <exit_code range="1:" level="fatal" description="Failure" />
11 <command> 11 </stdio>
12 make_decoy.rb $fasta_file -o $output -P $prefix_string $append 12 <command>
13 </command> 13 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
14 14 </command>
15 <stdio> 15 <inputs>
16 <exit_code range="1:" level="fatal" description="Failure" /> 16 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
17 </stdio> 17 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
18 18 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
19 <inputs> 19 </inputs>
20 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> 20 <outputs>
21 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> 21 <data format="fasta" name="output" />
22 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> 22 </outputs>
23 </inputs> 23 <tests>
24 24 <test>
25 <outputs> 25 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
26 <data format="fasta" name="output" /> 26 <output name="output" format="fasta">
27 </outputs> 27 <assert_contents>
28 28 <has_text text="decoy_rp3" />
29 <tests> 29 </assert_contents>
30 <test> 30 </output>
31 <param name="fasta_file" value="testdb.fasta" format="fasta"/> 31 </test>
32 <output name="output" format="fasta"> 32 </tests>
33 <assert_contents> 33 <help>
34 <has_text text="decoy_rp3" />
35 </assert_contents>
36 </output>
37 </test>
38 </tests>
39
40
41
42 <help>
43 34
44 **What it does** 35 **What it does**
45 36
46 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches 37 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches
47 38
48 39
49 </help> 40 </help>
50
51 </tool> 41 </tool>