Mercurial > repos > peterjc > clinod
changeset 26:5f55bebfcf0e draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod commit acaced2b77f2789558b3d4c210ec373f8bdbb7e9-dirty
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 18:32:12 -0400 |
| parents | 18f705de28ab |
| children | 074070ddf493 |
| files | tools/clinod/README.rst tools/clinod/clinod.xml |
| diffstat | 2 files changed, 5 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/clinod/README.rst Wed May 10 12:38:05 2017 -0400 +++ b/tools/clinod/README.rst Thu May 11 18:32:12 2017 -0400 @@ -73,6 +73,8 @@ v0.0.8 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.9 - Explicitly record clinod version via ``<version_command>``. +v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/clinod/clinod.xml Wed May 10 12:38:05 2017 -0400 +++ b/tools/clinod/clinod.xml Thu May 11 18:32:12 2017 -0400 @@ -1,23 +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="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>