Mercurial > repos > peterjc > seq_select_by_id
changeset 14:9c2b10d7b8ac draft
Uploaded v0.0.9, embeds citation, better naming of outputs
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 08:32:19 -0500 |
| parents | bedfe8f3d3fb |
| children | 1fc238a9fa95 |
| 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, 19 insertions(+), 22 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/seq_select_by_id/README.rst Wed Nov 20 12:13:14 2013 -0500 +++ b/tools/seq_select_by_id/README.rst Fri Nov 21 08:32:19 2014 -0500 @@ -1,7 +1,7 @@ Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID =============================================================== -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -36,20 +36,20 @@ There are just two files to install to use this tool from within Galaxy: -* seq_select_by_id.py (the Python script) -* seq_select_by_id.xml (the Galaxy tool definition) +* ``seq_select_by_id.py`` (the Python script) +* ``seq_select_by_id.xml`` (the Galaxy tool definition) -The suggested location is a dedicated tools/seq_select_by_id folder. +The suggested location is a dedicated ``tools/seq_select_by_id`` folder. -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. One suggested location is in the filters section. Simply add the line:: <tool file="seq_select_by_id/seq_select_by_id.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id seq_select_by_id + $ ./run_tests.sh -id seq_select_by_id You will also need to install Biopython 1.54 or later. That's it. @@ -73,7 +73,10 @@ - Fixed Biopython dependency setup. - Development moved to GitHub, https://github.com/peterjc/pico_galaxy - Renamed folder and adopted README.rst naming. -v0.0.8 - Corrected automated dependency definition +v0.0.8 - Corrected automated dependency definition. +v0.0.9 - Simplified XML to apply input format to output data. + - Tool definition now embeds citation information. + - Include input dataset name in output dataset names. ======= ======================================================================
--- a/tools/seq_select_by_id/seq_select_by_id.xml Wed Nov 20 12:13:14 2013 -0500 +++ b/tools/seq_select_by_id/seq_select_by_id.xml Fri Nov 21 08:32:19 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6"> +<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.9"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.62">biopython</requirement> @@ -19,17 +19,7 @@ <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> </inputs> <outputs> - <data name="output_file" format="fasta" label="Selected sequences"> - <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> - <change_format> - <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> - <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> - <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> - <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> - <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> - <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> - </change_format> - </data> + <data name="output_file" format="input" metadata_source="input_file" label="Selected sequences from $input_file.name"/> </outputs> <tests> <test> @@ -69,4 +59,8 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </citations> </tool>
--- a/tools/seq_select_by_id/tool_dependencies.xml Wed Nov 20 12:13:14 2013 -0500 +++ b/tools/seq_select_by_id/tool_dependencies.xml Fri Nov 21 08:32:19 2014 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.62"> - <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>