diff tools/protein_analysis/rxlr_motifs.xml @ 16:7de64c8b258d draft

Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub

--- a/tools/protein_analysis/rxlr_motifs.xml	Thu Apr 25 12:25:52 2013 -0400
+++ b/tools/protein_analysis/rxlr_motifs.xml	Wed Sep 18 06:16:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.6">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.7">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
     <command interpreter="python">
       rxlr_motifs.py $fasta_file 8 $model $tabular_file
@@ -32,6 +32,21 @@
             <param name="model" value="Win2007" />
             <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
+            <param name="model" value="Bhattacharjee2006"/>
+            <output name="tabular_file" file="empty_rxlr.Bhattacharjee2006.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
+            <param name="model" value="Win2007"/>
+            <output name="tabular_file" file="empty_rxlr.Win2007.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
+            <param name="model" value="Whisson2007"/>
+            <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
+        </test>
     </tests>
     <help>
     
@@ -59,9 +74,9 @@
 Looks for the oomycete motif RXLR as described in Bhattacharjee et al. (2006).
 
 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
-a SignalP Neural Network (NN) predicted clevage site giving a signal peptide
+a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
-after but within 100 amino acids of the clevage site.
+after but within 100 amino acids of the cleavage site.
 SignalP is run truncating the sequences to the first 70 amino acids, which was
 the default on the SignalP webservice used in Bhattacharjee et al. (2006).
 
@@ -71,9 +86,9 @@
 Looks for the protein motif RXLR as described in Win et al. (2007).
 
 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
-a SignalP Neural Network (NN) predicted clevage site giving a signal peptide
+a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
-after the clevage site and start between amino acids 30 and 60.
+after the cleavage site and start between amino acids 30 and 60.
 SignalP is run truncating the sequences to the first 70 amino acids, to match
 the methodology of Torto et al. (2003) followed in Win et al. (2007).
 
@@ -120,35 +135,45 @@
 
 **References**
 
-Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch
+If you use this Galaxy tool in work leading to a scientific publication please
+cite Cock et al. (2013) and the appropriate method paper(s):
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch (2007).
 A translocation signal for delivery of oomycete effector proteins into host plant cells.
-Nature 450:115-118, 2007.
+Nature 450:115-118.
 http://dx.doi.org/10.1038/nature06203
 
-Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun.
+Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun (2007).
 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.
-The Plant Cell 19:2349-2369, 2007.
+The Plant Cell 19:2349-2369.
 http://dx.doi.org/10.1105/tpc.107.051037
 
-Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar.
+Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar (2006).
 The malarial host-targeting signal is conserved in the Irish potato famine pathogen.
-PLoS Pathogens, 2(5):e50, 2006.
+PLoS Pathogens, 2(5):e50.
 http://dx.doi.org/10.1371/journal.ppat.0020050
 
-Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun.
+Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun (2003).
 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*.
-Genome Research, 13:1675-1685, 2003.
+Genome Research, 13:1675-1685.
 http://dx.doi.org/10.1101/gr.910003
 
-Sean R. Eddy.
+Sean R. Eddy (1998).
 Profile hidden Markov models.
-Bioinformatics, 14(9):755–763, 1998
+Bioinformatics, 14(9):755–763.
 http://dx.doi.org/10.1093/bioinformatics/14.9.755
 
-Nielsen, Engelbrecht, Brunak and von Heijne.
+Nielsen, Engelbrecht, Brunak and von Heijne (1997).
 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
-Protein Engineering, 10:1-6, 1997.
+Protein Engineering, 10:1-6.
 http://dx.doi.org/10.1093/protein/10.1.1
 
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
     </help>
 </tool>