Mercurial > repos > peterjc > effectivet3
changeset 28:d6976a4c055b draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
author | peterjc |
---|---|
date | Thu, 11 May 2017 12:44:17 -0400 |
parents | af14f755c05b |
children | 35c358aa7801 |
files | tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.xml |
diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/tools/effectiveT3/README.rst Thu May 11 10:06:00 2017 -0400 +++ b/tools/effectiveT3/README.rst Thu May 11 12:44:17 2017 -0400 @@ -96,6 +96,8 @@ - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar`` v0.0.17 - Update tool dependency definition to use cached URL. - Minor internal changes to Python script for error reporting & style. +v0.0.18 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/effectiveT3/effectiveT3.xml Thu May 11 10:06:00 2017 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Thu May 11 12:44:17 2017 -0400 @@ -1,22 +1,20 @@ -<tool id="effectiveT3" name="Effective T3" version="0.0.17"> +<tool id="effectiveT3" name="Effective T3" version="0.0.18"> <description>Find bacterial effectors in protein sequences</description> <requirements> <requirement type="package" version="1.0.1">effectiveT3</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">effectiveT3.py --version</version_command> - <command interpreter="python"> -effectiveT3.py $module.fields.path + <version_command> +python $__tool_directory__/effectiveT3.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/effectiveT3.py '$module.fields.path' #if $restrict.type=="cutoff": - cutoff=$restrict.cutoff + 'cutoff=$restrict.cutoff' #else: - $restrict.type + '$restrict.type' #end if -$fasta_file $tabular_file</command> +'$fasta_file' '$tabular_file' + </command> <inputs> <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> <param name="module" type="select" display="radio" label="Classification module">