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comparison tools/nlstradamus/nlstradamus.xml @ 4:1458e60f3fd0 draft

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v0.0.10 internal changes; v0.0.9 citation
author peterjc
date Wed, 05 Aug 2015 12:23:05 -0400
parents b2e648e55ed7
children
comparison
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3:b2e648e55ed7 4:1458e60f3fd0
1 <tool id="nlstradamus" name="NLStradamus" version="0.0.8"> 1 <tool id="nlstradamus" name="NLStradamus" version="0.0.10">
2 <description>Find nuclear localization signals (NLSs) in protein sequences</description> 2 <description>Find nuclear localization signals (NLSs) in protein sequences</description>
3 <command> 3 <requirements>
4 NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file 4 <requirement type="binary">NLStradamus</requirement>
5 </command> 5 <requirement type="package" version="1.8">NLStradamus</requirement>
6 </requirements>
6 <stdio> 7 <stdio>
7 <!-- Assume anything other than zero is an error --> 8 <!-- Assume anything other than zero is an error -->
8 <exit_code range="1:" /> 9 <exit_code range="1:" />
9 <exit_code range=":-1" /> 10 <exit_code range=":-1" />
10 </stdio> 11 </stdio>
12 <command>
13 NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
14 </command>
11 <inputs> 15 <inputs>
12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 16 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
13 <param name="model" type="select" display="radio" label="Model"> 17 <param name="model" type="select" display="radio" label="Model">
14 <option value="1" selected="True">Two state</option> 18 <option value="1" selected="True">Two state</option>
15 <option value="2">Four state</option> 19 <option value="2">Four state</option>
24 </param> 28 </param>
25 </inputs> 29 </inputs>
26 <outputs> 30 <outputs>
27 <data name="tabular_file" format="tabular" label="NLStradamus results" /> 31 <data name="tabular_file" format="tabular" label="NLStradamus results" />
28 </outputs> 32 </outputs>
29 <requirements>
30 <requirement type="binary">NLStradamus</requirement>
31 <requirement type="package" version="1.8">NLStradamus</requirement>
32 </requirements>
33 <tests> 33 <tests>
34 <test> 34 <test>
35 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> 35 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
36 <param name="model" value="1" /> 36 <param name="model" value="1" />
37 <param name="algorithm" value="1" /> 37 <param name="algorithm" value="1" />
38 <param name="threshold" value="0.6" /> 38 <param name="threshold" value="0.6" />
39 <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" /> 39 <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
40 </test> 40 </test>
41 <test> 41 <test>
42 <param name="fasta_file" value="empty.fasta" ftype="fasta" /> 42 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
43 <param name="model" value="2" /> 43 <param name="model" value="2" />
88 See also http://www.moseslab.csb.utoronto.ca/NLStradamus 88 See also http://www.moseslab.csb.utoronto.ca/NLStradamus
89 89
90 This wrapper is available to install into other Galaxy Instances via the Galaxy 90 This wrapper is available to install into other Galaxy Instances via the Galaxy
91 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus 91 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
92 </help> 92 </help>
93 <citations>
94 <citation type="doi">10.7717/peerj.167</citation>
95 <citation type="doi">10.1186/1471-2105-10-202</citation>
96 </citations>
93 </tool> 97 </tool>