Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/rxlr_motifs.xml @ 18:eb6ac44d4b8e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Suite v0.2.8, record Promoter 2 verion + misc internal updates
author peterjc
date Tue, 01 Sep 2015 09:56:36 -0400
parents e6cc27d182a8
children a19b3ded8f33
comparison
equal deleted inserted replaced
17:e6cc27d182a8 18:eb6ac44d4b8e
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.9"> 1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.11">
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 <requirements>
4 rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file" 4 <!-- Need SignalP for all the models -->
5 </command> 5 <requirement type="binary">signalp</requirement>
6 <requirement type="package">signalp</requirement>
7 <!-- Need HMMER for Whisson et al. (2007) -->
8 <requirement type="binary">hmmsearch</requirement>
9 <requirement type="package">hmmsearch</requirement>
10 </requirements>
6 <stdio> 11 <stdio>
7 <!-- Anything other than zero is an error --> 12 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 13 <exit_code range="1:" />
9 <exit_code range=":-1" /> 14 <exit_code range=":-1" />
10 </stdio> 15 </stdio>
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>
11 <inputs> 20 <inputs>
12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" /> 21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" />
13 <param name="model" type="select" label="Which RXLR model?"> 22 <param name="model" type="select" label="Which RXLR model?">
14 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option> 23 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
15 <option value="Win2007">Win et al. (2007) RXLR</option> 24 <option value="Win2007">Win et al. (2007) RXLR</option>
17 </param> 26 </param>
18 </inputs> 27 </inputs>
19 <outputs> 28 <outputs>
20 <data name="tabular_file" format="tabular" label="$model.value_label" /> 29 <data name="tabular_file" format="tabular" label="$model.value_label" />
21 </outputs> 30 </outputs>
22 <requirements>
23 <!-- Need SignalP for all the models -->
24 <requirement type="binary">signalp</requirement>
25 <!-- Need HMMER for Whisson et al. (2007) -->
26 <requirement type="binary">hmmsearch</requirement>
27 </requirements>
28 <tests> 31 <tests>
29 <test> 32 <test>
30 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" /> 33 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" />
31 <param name="model" value="Win2007" /> 34 <param name="model" value="Win2007" />
32 <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" /> 35 <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" />