Mercurial > repos > peterjc > clinod
diff tools/clinod/clinod.xml @ 7:f61366a4a14e draft
v0.0.10 Internal changes to command line handling
author | peterjc |
---|---|
date | Tue, 16 May 2017 08:50:43 -0400 |
parents | 77cfe958b5ea |
children | 4863b1dbe8f0 |
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--- a/tools/clinod/clinod.xml Tue Sep 01 06:54:03 2015 -0400 +++ b/tools/clinod/clinod.xml Tue May 16 08:50:43 2017 -0400 @@ -1,24 +1,18 @@ -<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9"> +<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10"> <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> <requirements> - <requirement type="binary">java</requirement> <requirement type="package" version="1.3">clinod</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <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" </version_command> - <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="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence +java -jar \$CLINOD/clinod-1.3.jar -in='$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>