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comparison tools/protein_analysis/rxlr_motifs.xml @ 20:a19b3ded8f33 draft

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v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
parents eb6ac44d4b8e
children 238eae32483c
comparison
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19:f3ecd80850e2 20:a19b3ded8f33
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.11"> 1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.14">
2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description> 2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
3 <requirements> 3 <requirements>
4 <!-- Need SignalP for all the models --> 4 <!-- Need SignalP for all the models -->
5 <requirement type="binary">signalp</requirement>
6 <requirement type="package">signalp</requirement> 5 <requirement type="package">signalp</requirement>
7 <!-- Need HMMER for Whisson et al. (2007) --> 6 <!-- Need HMMER for Whisson et al. (2007) -->
8 <requirement type="binary">hmmsearch</requirement> 7 <requirement type="package">hmmer2</requirement>
9 <requirement type="package">hmmsearch</requirement>
10 </requirements> 8 </requirements>
11 <stdio> 9 <version_command>
12 <!-- Anything other than zero is an error --> 10 python $__tool_directory__/rxlr_motifs.py -v
13 <exit_code range="1:" /> 11 </version_command>
14 <exit_code range=":-1" /> 12 <command detect_errors="aggressive">
15 </stdio> 13 python $__tool_directory__/rxlr_motifs.py '$fasta_file' "\$GALAXY_SLOTS" '$model' '$tabular_file'
16 <version_command interpreter="python">rxlr_motifs.py -v</version_command>
17 <command interpreter="python">
18 rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
19 </command> 14 </command>
20 <inputs> 15 <inputs>
21 <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" />
22 <param name="model" type="select" label="Which RXLR model?"> 17 <param name="model" type="select" label="Which RXLR model?">
23 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option> 18 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
24 <option value="Win2007">Win et al. (2007) RXLR</option> 19 <option value="Win2007">Win et al. (2007) RXLR</option>
25 <option value="Whisson2007" selected="True">Whisson et al. (2007) RXLR-EER with HMM</option> 20 <option value="Whisson2007" selected="true">Whisson et al. (2007) RXLR-EER with HMM</option>
26 </param> 21 </param>
27 </inputs> 22 </inputs>
28 <outputs> 23 <outputs>
29 <data name="tabular_file" format="tabular" label="$model.value_label" /> 24 <data name="tabular_file" format="tabular" label="$model.value_label" />
30 </outputs> 25 </outputs>
49 <param name="model" value="Whisson2007"/> 44 <param name="model" value="Whisson2007"/>
50 <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/> 45 <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
51 </test> 46 </test>
52 </tests> 47 </tests>
53 <help> 48 <help>
54 49
55 **Background** 50 **Background**
56 51
57 Many effector proteins from oomycete plant pathogens for manipulating the host 52 Many effector proteins from oomycete plant pathogens for manipulating the host
58 have been found to contain a signal peptide followed by a conserved RXLR motif 53 have been found to contain a signal peptide followed by a conserved RXLR motif
59 (Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There 54 (Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There