Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader
diff gene_family_scaffold_loader.xml @ 0:6282484a52bc draft
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author | greg |
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date | Tue, 21 Aug 2018 12:57:00 -0400 |
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children | 794951c24c86 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene_family_scaffold_loader.xml Tue Aug 21 12:57:00 2018 -0400 @@ -0,0 +1,45 @@ +<tool id="plant_tribes_gene_family_scaffold_loader" name="Load PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0"> + <description>into Galaxy PlantTribes database</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/gene_family_scaffold_loader.py' +--database_connection_string '$__app__.config.plant_tribes_database_connection' +--output '$output' +--scaffold_path '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold' +--output '$output']]></command> + <inputs> + <expand macro="param_scaffold" /> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <!--Testing this tool is a bit difficult at the current time.--> + </test> + </tests> + <help> +This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary +analyses of genome-scale gene families and transcriptomes. This tool analyzes scaffolds installed into Galaxy by the +PlantTribes Scaffolds Downloader data manager tool and inserts information about them into the Galaxy PlantTribes database +for querying and additional analysis. + +----- + +**Required options** + + * **Gene family scaffold** - one of the PlantTribes gene family scaffolds, installed into Galaxy by the PlantTribes Scaffold Data Manager tool, that has not yet been analyzed and loaded into the Galaxy PlantTribes database. + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {Greg Von Kuster,Eric Wafula}, + title = {None}, + year = {None}, + eprint = {None}, + url = {https://github.com/dePamphilis/PlantTribes}} + </citation> + </citations> +</tool>