Mercurial > repos > earlhaminst > ete
diff ete_genetree_splitter.xml @ 3:077021c45b96 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
| author | earlhaminst |
|---|---|
| date | Mon, 12 Mar 2018 12:51:48 -0400 |
| parents | |
| children | f1eca1158f21 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_genetree_splitter.xml Mon Mar 12 12:51:48 2018 -0400 @@ -0,0 +1,123 @@ +<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@.1"> + <description>from a genetree using the ETE Toolkit</description> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +python '$__tool_directory__/ete_genetree_splitter.py' +--genetree '$genetreeFile' +--gene_node $gene_node +#if $gainlose_conditional.gainlose == "True" + --speciestree '$gainlose_conditional.speciesFile' + --species_format $gainlose_conditional.species_format + --gainlose +#end if +--output_format $output_format + ]]></command> + <inputs> + <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" /> + <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option"> + <option value="0" selected="true">gene_species</option> + <option value="1">species_gene</option> + </param> + <conditional name="gainlose_conditional"> + <param name="gainlose" type="select" label="Find out gene gain/lose"> + <option value="True">Yes</option> + <option value="False" selected="true">No</option> + </param> + <when value="False" /> + <when value="True"> + <param name="speciesFile" type="data" format="nhx" label="Species file" help="Species Tree in nhx format" /> + <param name="species_format" type="select" label="Input species tree format" help="See table below"> + <option value="0">Flexible with support values (0)</option> + <option value="1">Flexible with internal node names (1)</option> + <option value="2">All branches + leaf names + internal supports (2)</option> + <option value="3">All branches + all names (3)</option> + <option value="4">Leaf branches + leaf names (4)</option> + <option value="5">Internal and leaf branches + leaf names (5)</option> + <option value="6">Internal branches + leaf names (6)</option> + <option value="7">Leaf branches + all names (7)</option> + <option value="8" selected="true">All names (8)</option> + <option value="9">Leaf names (9)</option> + <option value="100">Topology only (100)</option> + </param> + </when> + </conditional> + + <param name="output_format" type="select" label="Output GeneTree format" help="See table below"> + <option value="0">Flexible with support values (0)</option> + <option value="1">Flexible with internal node names (1)</option> + <option value="2">All branches + leaf names + internal supports (2)</option> + <option value="3">All branches + all names (3)</option> + <option value="4">Leaf branches + leaf names (4)</option> + <option value="5">Internal and leaf branches + leaf names (5)</option> + <option value="6">Internal branches + leaf names (6)</option> + <option value="7">Leaf branches + all names (7)</option> + <option value="8">All names (8)</option> + <option value="9" selected="true">Leaf names (9)</option> + <option value="100">Topology only (100)</option> + </param> + </inputs> + <outputs> + <collection name="genetrees_lists" type="list" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)_genetree\.nhx" ext="nhx" /> + </collection> + </outputs> + <tests> + <test> + <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> + <param name="gene_node" value="0"/> + <param name="output_format" value="9" /> + <output_collection name="genetrees_lists" type="list" count="4"> + <element name="1" file="11_genetree.nhx" ftype="nhx" /> + <element name="2" file="12_genetree.nhx" ftype="nhx" /> + <element name="3" file="13_genetree.nhx" ftype="nhx" /> + <element name="4" file="14_genetree.nhx" ftype="nhx" /> + </output_collection> + </test> + <test> + <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> + <param name="gene_node" value="0"/> + <param name="gainlose" value="True" /> + <param name="speciesFile" ftype="nhx" value="speciestree.nhx" /> + <param name="species_format" value="8" /> + <param name="output_format" value="9" /> + <output_collection name="genetrees_lists" type="list" count="5"> + <element name="1" file="21_genetree.nhx" ftype="nhx" /> + <element name="2" file="22_genetree.nhx" ftype="nhx" /> + <element name="3" file="23_genetree.nhx" ftype="nhx" /> + <element name="4" file="24_genetree.nhx" ftype="nhx" /> + <element name="5" file="25_genetree.nhx" ftype="nhx" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_. + +.. _ETE Toolkit: http://etetoolkit.org/ + +**Output format:** + +======= ============================================= ======================================================================================== +FORMAT DESCRIPTION SAMPLE +------- --------------------------------------------- ---------------------------------------------------------------------------------------- +0 flexible with support values ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788); +1 flexible with internal node names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788); +2 all branches + leaf names + internal supports ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788); +3 all branches + all names ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788); +4 leaf branches + leaf names ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049)); +5 internal and leaf branches + leaf names ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788); +6 internal branches + leaf names ((D,F):0.067192,(B,H):0.807788); +7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B); +8 all names ((D,F)E,(B,H)B); +9 leaf names ((D,F),(B,H)); +100 topology only ((,),(,)); +======= ============================================= ======================================================================================== + ]]></help> + <expand macro="citations" /> +</tool>