Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader
comparison 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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1 <tool id="plant_tribes_gene_family_scaffold_loader" name="Load PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0"> | |
2 <description>into Galaxy PlantTribes database</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 python '$__tool_directory__/gene_family_scaffold_loader.py' | |
8 --database_connection_string '$__app__.config.plant_tribes_database_connection' | |
9 --output '$output' | |
10 --scaffold_path '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold' | |
11 --output '$output']]></command> | |
12 <inputs> | |
13 <expand macro="param_scaffold" /> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="output" format="txt"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <!--Testing this tool is a bit difficult at the current time.--> | |
21 </test> | |
22 </tests> | |
23 <help> | |
24 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary | |
25 analyses of genome-scale gene families and transcriptomes. This tool analyzes scaffolds installed into Galaxy by the | |
26 PlantTribes Scaffolds Downloader data manager tool and inserts information about them into the Galaxy PlantTribes database | |
27 for querying and additional analysis. | |
28 | |
29 ----- | |
30 | |
31 **Required options** | |
32 | |
33 * **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. | |
34 </help> | |
35 <citations> | |
36 <citation type="bibtex"> | |
37 @unpublished{None, | |
38 author = {Greg Von Kuster,Eric Wafula}, | |
39 title = {None}, | |
40 year = {None}, | |
41 eprint = {None}, | |
42 url = {https://github.com/dePamphilis/PlantTribes}} | |
43 </citation> | |
44 </citations> | |
45 </tool> |