Mercurial > repos > earlhaminst > ete
comparison ete_gene_cnv.xml @ 8:16e925bf567e draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
| author | earlhaminst |
|---|---|
| date | Thu, 31 Oct 2019 07:48:59 -0400 |
| parents | |
| children | d40b9a7debe5 |
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| 7:6a5282f71f82 | 8:16e925bf567e |
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| 1 <tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@"> | |
| 2 <description>from a genetree using the ETE Toolkit</description> | |
| 3 <macros> | |
| 4 <import>ete_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 python '$__tool_directory__/ete_gene_cnv.py' | |
| 9 --genetree '$genetreeFile' | |
| 10 --speciesorder '$speciesorder' | |
| 11 > '$genes' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" /> | |
| 15 <param name="speciesorder" type="text" label="Species in order" help="Comma-separated species list" /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="genes" format="tabular" label="${tool.name} on ${on_string}"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="genetreeFile" ftype="nhx" value="test.nhx" /> | |
| 23 <param name="speciesorder" value="w,x,y,z,zz" /> | |
| 24 <output name="genes" file="test.tsv" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 Find copy number for genes from GeneTree by utilising the `ETE Toolkit`_. Input can be single GeneTree or multiple GeneTree in a file with one GeneTree per line. | |
| 29 | |
| 30 .. _ETE Toolkit: http://etetoolkit.org/ | |
| 31 ]]></help> | |
| 32 <expand macro="citations" /> | |
| 33 </tool> |