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comparison tools/protein_analysis/rxlr_motifs.xml @ 7:5e62aefb2918 draft

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Uploaded v0.1.2 to Test Tool Shed
author peterjc
date Tue, 26 Mar 2013 14:24:56 -0400
parents 39a6e46cdda3
children af3174637834
comparison
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6:39a6e46cdda3 7:5e62aefb2918
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.5"> 1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.6">
2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description> 2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 rxlr_motifs.py $fasta_file 8 $model $tabular_file 4 rxlr_motifs.py $fasta_file 8 $model $tabular_file
5 ##I want the number of threads to be a Galaxy config option... 5 ##I want the number of threads to be a Galaxy config option...
6 </command> 6 </command>
7 <stdio>
8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" />
10 <exit_code range=":-1" />
11 </stdio>
7 <inputs> 12 <inputs>
8 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" /> 13 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" />
9 <param name="model" type="select" label="Which RXLR model?"> 14 <param name="model" type="select" label="Which RXLR model?">
10 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option> 15 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
11 <option value="Win2007">Win et al. (2007) RXLR</option> 16 <option value="Win2007">Win et al. (2007) RXLR</option>
30 </tests> 35 </tests>
31 <help> 36 <help>
32 37
33 **Background** 38 **Background**
34 39
35 Many effector proteins from Oomycete plant pathogens for manipulating the host 40 Many effector proteins from oomycete plant pathogens for manipulating the host
36 have been found to contain a signal peptide followed by a conserved RXLR motif 41 have been found to contain a signal peptide followed by a conserved RXLR motif
37 (Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There 42 (Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There
38 are stiking parallels with the malarial host-targeting signal (Plasmodium 43 are striking parallels with the malarial host-targeting signal (Plasmodium
39 export element, or "Pexel" for short). 44 export element, or "Pexel" for short).
40 45
41 ----- 46 -----
42 47
43 **What it does** 48 **What it does**