Mercurial > repos > earlhaminst > ete
changeset 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 | 276e3ee68c37 |
| children | 03c10736e497 |
| files | ete_species_tree_generator.py ete_species_tree_generator.xml ete_tree_generator.py ete_tree_generator.xml |
| diffstat | 4 files changed, 146 insertions(+), 146 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_species_tree_generator.py Fri Mar 17 16:23:39 2017 -0400 @@ -0,0 +1,56 @@ +import optparse + +from ete3 import NCBITaxa + +ncbi = NCBITaxa() + +parser = optparse.OptionParser() +parser.add_option('-s', '--species', dest="input_species_filename", + help='Species list in text format one species in each line') + +parser.add_option('-f', '--format', type='choice', choices=['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '100'], dest="format", + default='8', help='outpur format for tree') + +parser.add_option('-t', '--treebest', type='choice', choices=['yes', 'no'], dest="treebest", + default='no', help='To be used in TreeBest') + +parser.add_option('-d', '--database', type='choice', choices=['yes', 'no'], dest="database", + default='no', help='Update database') + +options, args = parser.parse_args() + +if options.database == "yes": + try: + ncbi.update_taxonomy_database() + except: + pass + +if options.input_species_filename is None: + raise Exception('-s option must be specified, Species list in text format one species in each line') + +with open(options.input_species_filename) as f: + species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] + +name2taxid = ncbi.get_name_translator(species_name) + +taxid = [name2taxid[_][0] for _ in species_name] + +tree = ncbi.get_topology(taxid) + +if options.treebest == "yes": + inv_map = {str(v[0]): k.replace(" ", "") + "*" for k, v in name2taxid.items()} +else: + inv_map = {str(v[0]): k for k, v in name2taxid.items()} + + +for leaf in tree: + leaf.name = inv_map[leaf.name] + +newickTree = tree.write(format=int(options.format)) + +if options.treebest == "yes": + newickTree = newickTree.rstrip(';') + newickTree = newickTree + "root;" + +with open('newickTree.nhx', 'w') as newickFile: + newickFile.write(newickTree)
--- /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>
--- a/ete_tree_generator.py Thu Dec 15 12:55:02 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -import optparse - -from ete3 import NCBITaxa - -ncbi = NCBITaxa() - -parser = optparse.OptionParser() -parser.add_option('-s', '--species', dest="input_species_filename", - help='Species list in text format one species in each line') - -parser.add_option('-f', '--format', type='choice', choices=['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '100'], dest="format", - default='8', help='outpur format for tree') - -parser.add_option('-t', '--treebest', type='choice', choices=['yes', 'no'], dest="treebest", - default='no', help='To be used in TreeBest') - -parser.add_option('-d', '--database', type='choice', choices=['yes', 'no'], dest="database", - default='no', help='Update database') - -options, args = parser.parse_args() - -if options.database == "yes": - try: - ncbi.update_taxonomy_database() - except: - pass - -if options.input_species_filename is None: - raise Exception('-s option must be specified, Species list in text format one species in each line') - -with open(options.input_species_filename) as f: - species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] - -name2taxid = ncbi.get_name_translator(species_name) - -taxid = [name2taxid[_][0] for _ in species_name] - -tree = ncbi.get_topology(taxid) - -if options.treebest == "yes": - inv_map = {str(v[0]): k.replace(" ", "") + "*" for k, v in name2taxid.items()} -else: - inv_map = {str(v[0]): k for k, v in name2taxid.items()} - - -for leaf in tree: - leaf.name = inv_map[leaf.name] - -newickTree = tree.write(format=int(options.format)) - -if options.treebest == "yes": - newickTree = newickTree.rstrip(';') - newickTree = newickTree + "root;" - -with open('newickTree.nhx', 'w') as newickFile: - newickFile.write(newickTree)
--- a/ete_tree_generator.xml Thu Dec 15 12:55:02 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<tool id="species_tree_generator" name="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 $__tool_directory__/ete_tree_generator.py --s '$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>