Mercurial > repos > earlhaminst > ete
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_gene_cnv.xml Thu Oct 31 07:48:59 2019 -0400 @@ -0,0 +1,33 @@ +<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@"> + <description>from a genetree using the ETE Toolkit</description> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/ete_gene_cnv.py' +--genetree '$genetreeFile' +--speciesorder '$speciesorder' +> '$genes' + ]]></command> + <inputs> + <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" /> + <param name="speciesorder" type="text" label="Species in order" help="Comma-separated species list" /> + </inputs> + <outputs> + <data name="genes" format="tabular" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="genetreeFile" ftype="nhx" value="test.nhx" /> + <param name="speciesorder" value="w,x,y,z,zz" /> + <output name="genes" file="test.tsv" /> + </test> + </tests> + <help><![CDATA[ +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. + +.. _ETE Toolkit: http://etetoolkit.org/ + ]]></help> + <expand macro="citations" /> +</tool>