Mercurial > repos > peterjc > seq_composition
changeset 4:13be788233da draft default tip
v0.0.5 Internal changes to command line handling
| author | peterjc |
|---|---|
| date | Tue, 16 May 2017 09:26:26 -0400 |
| parents | 7a26bb458806 |
| children | |
| files | tools/seq_composition/README.rst tools/seq_composition/seq_composition.xml |
| diffstat | 2 files changed, 9 insertions(+), 11 deletions(-) [+] |
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--- a/tools/seq_composition/README.rst Wed May 10 13:03:42 2017 -0400 +++ b/tools/seq_composition/README.rst Tue May 16 09:26:26 2017 -0400 @@ -42,7 +42,7 @@ You will also need to install Biopython 1.62 or later. -If you wish to run the unit tests, also move/copy the ``test-data/`` files +If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: ./run_tests.sh -id seq_composition @@ -62,6 +62,8 @@ - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.3 - Python style updates (internal change only). v0.0.4 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. +v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/seq_composition/seq_composition.xml Wed May 10 13:03:42 2017 -0400 +++ b/tools/seq_composition/seq_composition.xml Tue May 16 09:26:26 2017 -0400 @@ -1,19 +1,15 @@ -<tool id="seq_composition" name="Sequence composition" version="0.0.4"> +<tool id="seq_composition" name="Sequence composition" version="0.0.5"> <description>Count bases or amino-acids</description> <requirements> <requirement type="package" version="1.67">biopython</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">seq_composition.py --version</version_command> - <command interpreter="python"> -seq_composition.py -o "$output_file" + <version_command> +python $__tool_directory__/seq_composition.py --version</version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/seq_composition.py -o '$output_file' ##For loop over inputs #for i in $input_file ---$i.ext "${i}" +--$i.ext '${i}' #end for </command> <inputs>