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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 19:28:20 -0400
parents fa4ed0c996d9
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2:fa4ed0c996d9 3:84b15e316fcc
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 <requirement type="package" version="1.3">protk</requirement> 3 Generate random protein sequences with the same AA composition as input sequences
4 </requirements> 4 </description>
5 5 <requirements>
6 <description> 6 <container type="docker">iracooke/protk-1.4.3</container>
7 Generate random protein sequences with the same AA composition as input sequences 7 <requirement type="package" version="1.4.3">protk</requirement>
8 </description> 8 </requirements>
9 9 <stdio>
10 <command> 10 <exit_code range="1:" level="fatal" description="Failure" />
11 make_decoy.rb $fasta_file -o $output -P $prefix_string $append 11 </stdio>
12 </command> 12 <command>
13 13 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
14 <stdio> 14 </command>
15 <exit_code range="1:" level="fatal" description="Failure" /> 15 <inputs>
16 </stdio> 16 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
17 17 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
18 <inputs> 18 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
19 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> 19 </inputs>
20 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> 20 <outputs>
21 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> 21 <data format="fasta" name="output" />
22 </inputs> 22 </outputs>
23 23 <tests>
24 <outputs> 24 <test>
25 <data format="fasta" name="output" /> 25 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
26 </outputs> 26 <output name="output" format="fasta">
27 27 <assert_contents>
28 28 <has_text text="decoy_rp3" />
29 <help> 29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help>
30 34
31 **What it does** 35 **What it does**
32 36
33 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
34 38
35 39
36 </help> 40 </help>
37
38 </tool> 41 </tool>