diff tools/clinod/clinod.xml @ 8:4863b1dbe8f0 draft

"Update all the pico_galaxy tools on main Tool Shed"

--- a/tools/clinod/clinod.xml	Tue May 16 08:50:43 2017 -0400
+++ b/tools/clinod/clinod.xml	Fri Apr 16 22:33:30 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.1.0">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.3">clinod</requirement>
@@ -6,17 +6,14 @@
     <version_command>
 ##The first non-blank line contains the version information, e.g.
 ##NucleOlar localization sequence Detector v. 1.3b (13 May 2011)
-##Question: Why don't we have to escape the dollar here?
-java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector"
+clinod | grep -i "^NucleOlar localization sequence Detector"
     </version_command>
     <command detect_errors="aggressive">
-##The Galaxy Tool Shed installation should define $CLINOD to point at folder
-##containing both clinod-1.3.jar and the batchman binary:
-java -jar \$CLINOD/clinod-1.3.jar -in='$fasta_file' -out='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence
+clinod -in='$fasta_file' -out='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <inputs>
-        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
     </inputs>
     <outputs>
         <data name="tabular_file" format="tabular" label="NoD results" />
@@ -28,7 +25,6 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This calls the command line version of the NoD tool from the Barton Group for
@@ -63,17 +59,17 @@
 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
+https://doi.org/10.7717/peerj.167
 
 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010).
 Characterization and prediction of protein nucleolar localization sequences.
 Nucleic Acids Research 38(21), 7388-7399.
-http://dx.doi.org/10.1093/nar/gkq653
+https://doi.org/10.1093/nar/gkq653
 
 M. S. Scott, P. V. Troshin and G. J. Barton (2011).
 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
 BMC Bioinformatics, 12:317.
-http://dx.doi.org/10.1186/1471-2105-12-317
+https://doi.org/10.1186/1471-2105-12-317
 
 See also http://www.compbio.dundee.ac.uk/www-nod/