Mercurial > repos > earlhaminst > ete
diff ete_species_tree_generator.xml @ 1:a4ba317fc713 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
| author | earlhaminst |
|---|---|
| date | Fri, 17 Mar 2017 16:23:39 -0400 |
| parents | |
| children | 03c10736e497 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_species_tree_generator.xml Fri Mar 17 16:23:39 2017 -0400 @@ -0,0 +1,90 @@ +<tool id="ete_species_tree_generator" name="ETE species tree generator" version="3.0.0b35"> + <description>from a list of species using the ETE Toolkit</description> + <requirements> + <requirement type="package" version="3.0.0b35">ete3</requirement> + </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ +python $__tool_directory__/ete_species_tree_generator.py +-s '$speciesFile' +#if $output_format.treebest == 'yes' + -f 8 +#else + -f ${output_format.format_selector} +#end if +-t $output_format.treebest +-d $database + ]]> + </command> + <inputs> + <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" /> + <conditional name="output_format"> + <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes" /> + <when value="no"> + <param name="format_selector" type="select" label="Output format" help="See table below"> + <option value="0" selected="true">Flexible with support values (0)</option> + <option value="1">Flexible with internal node names (1)</option> + <option value="2">All branches + leaf names + internal supports (2)</option> + <option value="3">All branches + all names (3)</option> + <option value="4">Leaf branches + leaf names (4)</option> + <option value="5">Internal and leaf branches + leaf names (5)</option> + <option value="6">Internal branches + leaf names (6)</option> + <option value="7">Leaf branches + all names (7)</option> + <option value="8">All names (8)</option> + <option value="9">Leaf names (9)</option> + <option value="100">Topology only (100)</option> + </param> + </when> + </conditional> + <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/> + </outputs> + <tests> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="treebest" value="yes" /> + <output name="outputFile" file="out.nhx" /> + </test> + </tests> + <help> + <![CDATA[ +Generate a species tree from a list of species 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> + <citations> + <citation type="doi">10.1093/molbev/msw046</citation> + </citations> +</tool>