Mercurial > repos > peterjc > seq_select_by_id
changeset 21:3dc9fd2ad70c draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
| author | peterjc |
|---|---|
| date | Fri, 21 Apr 2017 12:07:51 -0400 |
| parents | 6c5822581e41 |
| children | 3d392ef52a22 |
| files | tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.xml tools/seq_select_by_id/tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 12 deletions(-) [+] |
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--- a/tools/seq_select_by_id/README.rst Thu Feb 09 11:28:17 2017 -0500 +++ b/tools/seq_select_by_id/README.rst Fri Apr 21 12:07:51 2017 -0400 @@ -86,6 +86,8 @@ - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Quote filenames in case of spaces (internal change only). v0.0.12 - Python style changes (internal change only). + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. ======= ======================================================================
--- a/tools/seq_select_by_id/seq_select_by_id.xml Thu Feb 09 11:28:17 2017 -0500 +++ b/tools/seq_select_by_id/seq_select_by_id.xml Fri Apr 21 12:07:51 2017 -0400 @@ -1,17 +1,13 @@ <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.12"> <description>from a tabular file</description> <requirements> - <requirement type="package" version="1.62">biopython</requirement> - <requirement type="python-module">Bio</requirement> + <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_select_by_id.py --version</version_command> - <command interpreter="python"> -seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file" + <version_command> +python $__tool_directory__/seq_select_by_id.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/seq_select_by_id.py '$input_tabular' '$column' '$input_file' '$input_file.ext' '$output_file' </command> <inputs> <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
--- a/tools/seq_select_by_id/tool_dependencies.xml Thu Feb 09 11:28:17 2017 -0500 +++ b/tools/seq_select_by_id/tool_dependencies.xml Fri Apr 21 12:07:51 2017 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.62"> - <repository changeset_revision="76434ffd927d" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>