| Next changeset 1:d2d26d330236 (2012-04-11) |
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Commit message:
Migrated tool version 0.1 from old tool shed archive to new tool shed repository |
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added:
onto-toolkit/INSTALL onto-toolkit/README onto-toolkit/screenshots/ONTO-Toolkit.png onto-toolkit/suite_config.xml onto-toolkit/test-data/pre_cco_core.obo onto-toolkit/tool_conf.xml onto-toolkit/tools/ontology/get_ancestor_terms.xml onto-toolkit/tools/ontology/get_child_terms.xml onto-toolkit/tools/ontology/get_descendent_terms.xml onto-toolkit/tools/ontology/get_intersection_ontology_from.pl onto-toolkit/tools/ontology/get_intersection_ontology_from.xml onto-toolkit/tools/ontology/get_list_intersection_from.pl onto-toolkit/tools/ontology/get_list_intersection_from.xml onto-toolkit/tools/ontology/get_parent_terms.xml onto-toolkit/tools/ontology/get_relationship_types.xml onto-toolkit/tools/ontology/get_subontology_from.xml onto-toolkit/tools/ontology/obo2owl.xml onto-toolkit/tools/ontology/obo2rdf.xml onto-toolkit/tools/ontology/obo2tran.xml onto-toolkit/tools/ontology/term_id_vs_term_def.xml onto-toolkit/tools/ontology/term_id_vs_term_name.xml |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/INSTALL --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/INSTALL Tue Jun 07 17:51:45 2011 -0400 |
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| @@ -0,0 +1,41 @@ +INSTALL +======= + +ONTO-Toolkit requires: + +1. Galaxy (latest version recommended): + + http://main.g2.bx.psu.edu/ + +2. ONTO-PERL (version >= 1.18): + + http://search.cpan.org/dist/ONTO-PERL/ + +After installing the required software: + +1. Copy the '/ontology/*.xml' to '$GALAXY_HOME/tools/' + +2. Copy the test data file 'pre_cco_core.obo' to '$GALAXY_HOME/test-data/' + +3. Adapt your 'tool_conf.xml' file by adding the 'ONTO-ToolKit' section: + + <section name="OBO Ontology manipulation" id="ONTO-ToolKit"> + <tool file="ontology/get_ancestor_terms.xml"/> + <tool file="ontology/get_parent_terms.xml"/> + <tool file="ontology/get_descendent_terms.xml"/> + <tool file="ontology/get_child_terms.xml"/> + <tool file="ontology/term_id_vs_term_def.xml"/> + <tool file="ontology/term_id_vs_term_name.xml"/> + <tool file="ontology/get_relationship_types.xml"/> + <tool file="ontology/obo2rdf.xml" /> + <tool file="ontology/obo2tran.xml" /> + <tool file="ontology/obo2owl.xml" /> + </section> + +4. Restart your Galaxy instance. + +Bugs/comments/questions/etc +=========================== + +ONTO-Toolkit is regularly updated, please report any bugs or +send your comments to erick.antezana -@- gmail.com \ No newline at end of file |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/README Tue Jun 07 17:51:45 2011 -0400 |
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| @@ -0,0 +1,41 @@ +README +====== + +ONTO-Toolkit is a collection of Galaxy tools for managing ontologies +that are represented in the OBO flat file format (spec 1.2). + +Those tools are basically wrappers around the most commonly used tasks +provided by the ONTO-PERL suite. + +See also: + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + Antezana E, Egana M, De Baets B, Kuiper M, Mironov V. + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + +For installing this collection of tools: + + see the file INSTALL + +DEPENDENCIES +============ + +ONTO-Toolkit requires: + +1. Galaxy (latest version is recommended): + + http://main.g2.bx.psu.edu/ + +2. ONTO-PERL (version >= 1.18): + + http://search.cpan.org/dist/ONTO-PERL/ + +COPYRIGHT AND LICENCE +===================== + +Copyright (c) 2010 Erick Antezana. All rights reserved. +OONTO-Toolkit is free software; you can redistribute it and/or +modify it under the same terms as Perl itself. + +N.B. Galaxy is distributed as open source under the conditions of the +Academic Free License (http://www.opensource.org/licenses/academic.php). \ No newline at end of file |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/screenshots/ONTO-Toolkit.png |
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| Binary file onto-toolkit/screenshots/ONTO-Toolkit.png has changed |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/suite_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/suite_config.xml Tue Jun 07 17:51:45 2011 -0400 |
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| @@ -0,0 +1,55 @@ +<suite id="ONTO-ToolKit" name="Suite of OBO Ontology manipulation tools" version="0.1"> + <description>This suite contains tools for managing ontologies that are represented in the OBO flat file format</description> + + <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.22"> + <description> Collects the ancestor terms from a given term in the given OBO ontology</description> + </tool> + + <tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.22"> + <description>Collects the child terms from a given term in the given OBO ontology</description> + </tool> + + <tool id="get_descendent_terms" name="Get the descendent terms of a given OBO term" version="1.22"> + <description>Collects the descendent terms from a given term in the given OBO ontology</description> + </tool> + + <tool id="get_intersection_ontology_from" name="Gets an intersection ontology from given OBO ontologies" version="1.22"> + <description>Provides an intersection of the given ontologies (in OBO format)</description> + </tool> + + <tool id="get_list_intersection_from" name="Get the overlapping terms from a given set OBO terms" version="1.22"> + <description>Collects common OBO terms from a given set of list containing OBO terms</description> + </tool> + + <tool id="get_parent_terms" name="Get the parent terms of a given OBO term" version="1.22"> + <description>Collects the parent terms from a given term in the given OBO ontology</description> + </tool> + + <tool id="get_relationship_types" name="Get all the relationship types in an ontology" version="1.22"> + <description>Collects the relationship types in the given OBO ontology</description> + </tool> + + <tool id="get_subontology_from" name="Get subontology from a given OBO term" version="1.22"> + <description>Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID</description> + </tool> + + <tool id="obo2owl" name="Convert OBO to OWL" version="1.22"> + <description>Converts an OBO formatted ontology to OWL format</description> + </tool> + + <tool id="obo2rdf" name="Convert OBO to RDF" version="1.22"> + <description>Converts an OBO formatted ontology to RDF/XML format</description> + </tool> + + <tool id="obo2tran" name="Convert OBO to RDF (tc)" version="1.22"> + <description>Converts an OBO formatted ontology to RDF/XML format with transitive closure</description> + </tool> + + <tool id="term_id_vs_term_def" name="Get all the term IDs and term definitions of a given OBO ontology" version="1.22"> + <description>Get all the term IDs and term definitions of a given OBO ontology</description> + </tool> + + <tool id="term_id_vs_term_name" name="Get all the term IDs and term names of a given OBO ontology" version="1.22"> + <description>Get all the term IDs and term names of a given OBO ontology</description> + </tool> +</suite> |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/test-data/pre_cco_core.obo --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/test-data/pre_cco_core.obo Tue Jun 07 17:51:45 2011 -0400 |
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| b'@@ -0,0 +1,3845 @@\n+format-version: 1.2\n+date: 16:02:2007 16:06\n+default-namespace: CCO\n+autogenerated-by: ONTO-PERL\n+remark: The Cell-Cycle Ontology\n+\n+[Term]\n+id: CCO:B0000000\n+name: core cell cycle protein\n+def: "A protein being considered as principal in the regulation of the cell cycle process" [CCO:cco_team]\n+is_a: CCO:U0000005 ! protein\n+\n+[Term]\n+id: CCO:P0000001\n+name: mitotic spindle elongation\n+def: "Lengthening of the distance between poles of the mitotic spindle." [GOC:mah]\n+is_a: CCO:P0000310 ! spindle elongation\n+relationship: part_of CCO:P0000058 ! mitotic spindle organization and biogenesis\n+synonym: "spindle elongation during mitosis" EXACT []\n+xref: GO:0000022\n+\n+[Term]\n+id: CCO:P0000002\n+name: mitotic sister chromatid segregation\n+def: "The cell cycle process whereby replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai]\n+is_a: CCO:P0000308 ! cell cycle process\n+relationship: part_of CCO:P0000069 ! mitosis\n+synonym: "mitotic chromosome segregation" EXACT []\n+synonym: "mitotic sister-chromatid adhesion release" NARROW []\n+xref: GO:0000070\n+xref: GO:0016359\n+\n+[Term]\n+id: CCO:P0000003\n+name: M phase specific microtubule process\n+def: "A microtubule-based process that occurs only during M phase of the cell cycle." [GOC:mah]\n+relationship: part_of CCO:P0000038 ! M phase\n+synonym: "M-phase specific microtubule process" EXACT []\n+xref: GO:0000072\n+\n+[Term]\n+id: CCO:P0000004\n+name: regulation of progression through cell cycle\n+def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:go_curators]\n+is_a: CCO:P0000294 ! regulation of cell cycle\n+synonym: "cell cycle regulator" RELATED []\n+synonym: "RHEB small monomeric GTPase activity" RELATED []\n+synonym: "tumor suppressor" RELATED []\n+synonym: "control of cell cycle progression" EXACT []\n+synonym: "modulation of cell cycle progression" EXACT []\n+synonym: "regulation of cell cycle progression" EXACT []\n+xref: Reactome:156678\n+xref: Reactome:156699\n+xref: Reactome:156711\n+xref: Reactome:162657\n+xref: Reactome:165167\n+xref: Reactome:167104\n+xref: Reactome:167109\n+xref: Reactome:169311\n+xref: Reactome:171117\n+xref: Reactome:171122\n+xref: Reactome:174455\n+xref: Reactome:177752\n+xref: Reactome:177757\n+xref: GO:0000074\n+\n+[Term]\n+id: CCO:P0000005\n+name: cell cycle checkpoint\n+def: "A point in the eukaryotic cell cycle where progress through the cycle can be halted until conditions are suitable for the cell to proceed to the next stage." [GOC:mah, ISBN:0815316194]\n+is_a: CCO:P0000004 ! regulation of progression through cell cycle\n+xref: Reactome:69620\n+xref: GO:0000075\n+\n+[Term]\n+id: CCO:P0000006\n+name: DNA replication checkpoint\n+def: "A signal transduction based surveillance mechanism that prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome." [GOC:rn, PMID:11728327, PMID:12537518]\n+is_a: CCO:P0000157 ! DNA integrity checkpoint\n+xref: GO:0000076\n+\n+[Term]\n+id: CCO:P0000007\n+name: DNA damage checkpoint\n+def: "A signal transduction pathway, induced by DNA damage, that blocks cell cycle progression (in G1, G2 or metaphase) or slows the rate at which S phase proceeds." [PMID:11891124]\n+is_a: CCO:P0000157 ! DNA integrity checkpoint\n+synonym: "DNA damage response, signal transduction resulting in cell cycle arrest" NARROW []\n+xref: GO:0000077\n+\n+[Term]\n+id: CCO:P0000008\n+name: cell morphogenesis checkpoint\n+def: "A cell cycle checkpoint observed when aspects of polarity control are defective, which maintains coordination between the process of cellular morphogenesis and the nuclear events of the cell cycle. For example, in budding yeast cell-cycle dela'..b' earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:preceded_by\n+\n+[Typedef]\n+id: precedes\n+name: precedes\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:precedes\n+\n+[Typedef]\n+id: proper_part_of\n+name: proper_part_of\n+def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]\n+is_a: part_of ! part_of\n+is_transitive: true\n+xref: OBO_REL:proper_part_of\n+\n+[Typedef]\n+id: relationship\n+name: relationship\n+def: "A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances." []\n+xref: OBO_REL:relationship\n+\n+[Typedef]\n+id: transformation_of\n+name: transformation_of\n+def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C\' if and only if given any c and any t, if c instantiates C at time t, then for some t\', c instantiates C\' at t\' and t\' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C\' at t2." [PMID:15892874]\n+comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: OBO_REL:transformation_of\n+\n+[Typedef]\n+id: transforms_into\n+name: transforms_into\n+is_a: relationship ! relationship\n+is_transitive: true\n+xref: CCO_REL:transforms_into\n+\n+[Typedef]\n+id: has_source\n+name: has_source\n+def: "o originates from O where o is a gene or gene product and O an organism." [CCO:ea]\n+is_a: relationship ! relationship\n+xref: CCO_REL:has_source\n+\n+[Typedef]\n+id: source_of\n+name: source_of\n+def: "O source of o where O is an organism and o a gene or gene product." [CCO:ea]\n+is_a: relationship ! relationship\n+xref: CCO_REL:source_of\n+\n+[Typedef]\n+id: has_function\n+name: has_function\n+is_a: relationship ! relationship\n+xref: OBO_REL:has_function\n' |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tool_conf.xml Tue Jun 07 17:51:45 2011 -0400 |
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| b'@@ -0,0 +1,364 @@\n+<?xml version="1.0"?>\n+<toolbox>\n+ <section name="Get Data" id="getext">\n+ <tool file="data_source/upload.xml"/>\n+ <tool file="data_source/ucsc_tablebrowser.xml" />\n+ <tool file="data_source/ucsc_tablebrowser_test.xml" /> \n+ <tool file="data_source/ucsc_tablebrowser_archaea.xml" />\n+ <tool file="data_source/bx_browser.xml" />\n+ <tool file="data_source/microbial_import.xml" />\n+ <tool file="data_source/biomart.xml" />\n+ <tool file="data_source/biomart_test.xml" />\n+ <tool file="data_source/gramene_mart.xml" />\n+ <tool file="data_source/flymine.xml" />\n+ <tool file="data_source/flymine_test.xml" />\n+ <tool file="data_source/modmine.xml" />\n+ <tool file="data_source/ratmine.xml" />\n+ <tool file="data_source/wormbase.xml" />\n+ <tool file="data_source/wormbase_test.xml" />\n+ <tool file="data_source/eupathdb.xml" />\n+ <tool file="data_source/encode_db.xml" />\n+ <tool file="data_source/epigraph_import.xml" />\n+ <tool file="data_source/epigraph_import_test.xml" />\n+ <tool file="data_source/hbvar.xml" /> \n+ <tool file="validation/fix_errors.xml" />\n+ </section>\n+ <section name="OBO Ontology manipulation" id="ONTO-ToolKit">\n+ <tool file="ontology/get_ancestor_terms.xml"/>\n+ <tool file="ontology/get_parent_terms.xml"/>\n+ <tool file="ontology/get_descendent_terms.xml"/>\n+ <tool file="ontology/get_child_terms.xml"/>\n+ <tool file="ontology/term_id_vs_term_def.xml"/>\n+ <tool file="ontology/term_id_vs_term_name.xml"/>\n+ <tool file="ontology/get_relationship_types.xml"/>\n+ <tool file="ontology/obo2rdf.xml" />\n+ <tool file="ontology/obo2tran.xml" />\n+ <tool file="ontology/obo2owl.xml" />\n+ <tool file="ontology/get_subontology_from.xml" />\n+ <tool file="ontology/get_list_intersection_from.xml" />\n+ <tool file="ontology/get_intersection_ontology_from.xml" />\n+ </section>\n+ <section name="Send Data" id="send">\n+ <tool file="data_destination/epigraph.xml" />\n+ <tool file="data_destination/epigraph_test.xml" />\n+ </section>\n+ <section name="ENCODE Tools" id="EncodeTools">\n+ <tool file="encode/gencode_partition.xml" />\n+ <tool file="encode/random_intervals.xml" />\n+ </section>\n+ <section name="Lift-Over" id="liftOver">\n+ <tool file="extract/liftOver_wrapper.xml" />\n+ </section>\n+ <section name="Text Manipulation" id="textutil">\n+ <tool file="filters/fixedValueColumn.xml" />\n+ <tool file="stats/column_maker.xml" />\n+ <tool file="filters/catWrapper.xml" />\n+ <tool file="filters/cutWrapper.xml" />\n+ <tool file="filters/mergeCols.xml" />\n+ <tool file="filters/convert_characters.xml" />\n+ <tool file="filters/CreateInterval.xml" />\n+ <tool file="filters/cutWrapper.xml" />\n+ <tool file="filters/changeCase.xml" />\n+ <tool file="filters/pasteWrapper.xml" />\n+ <tool file="filters/remove_beginning.xml" />\n+ <tool file="filters/headWrapper.xml" />\n+ <tool file="filters/tailWrapper.xml" />\n+ <tool file="filters/trimmer.xml" />\n+ <tool file="stats/dna_filtering.xml" />\n+ </section>\n+ <section name="Filter and Sort" id="filter">\n+ <tool file="stats/filtering.xml" />\n+ <tool file="filters/sorter.xml" />\n+ <tool file="filters/grep.xml" />\n+ </section>\n+ <section name="Join, Subtract and Group" id="group">\n+ <tool file="filters/joiner.xml" />\n+ <tool file="filters/compare.xml"/>\n+ <tool file="new_operations/subtract_query.xml"/>\n+ <tool file="stats/grouping.xml" /> \n+ </section>\n+ <section name="Convert Formats" id="convert">\n+ <tool file="filters/axt_to_concat_fasta.xml" />\n+ <tool file="filters/axt_to_fasta.xml" />\n+ <tool file="filters/axt_to_lav.xml" />\n+ <tool file="filters/bed2gff.xml" />\n+ <tool file="fasta_tools/fasta_to_tabular.xml" />\n+ <tool file="filters/gff2bed.xml" />\n+ <tool file="filters/lav_to_bed.xml" />\n+ <tool file="maf/maf_to_bed.xml" />\n+ <tool file="maf/maf_to_interval.xml" />\n+ <tool file="maf/maf'..b'file="emboss_5/emboss_dreg.xml" />\n+ <tool file="emboss_5/emboss_einverted.xml" />\n+ <tool file="emboss_5/emboss_epestfind.xml" />\n+ <tool file="emboss_5/emboss_equicktandem.xml" />\n+ <tool file="emboss_5/emboss_est2genome.xml" />\n+ <tool file="emboss_5/emboss_etandem.xml" />\n+ <tool file="emboss_5/emboss_extractfeat.xml" />\n+ <tool file="emboss_5/emboss_extractseq.xml" />\n+ <tool file="emboss_5/emboss_freak.xml" /> \n+ <tool file="emboss_5/emboss_fuzznuc.xml" />\n+ <tool file="emboss_5/emboss_fuzzpro.xml" />\n+ <tool file="emboss_5/emboss_fuzztran.xml" />\n+ <tool file="emboss_5/emboss_garnier.xml" />\n+ <tool file="emboss_5/emboss_geecee.xml" />\n+ <tool file="emboss_5/emboss_getorf.xml" />\n+ <tool file="emboss_5/emboss_helixturnhelix.xml" />\n+ <tool file="emboss_5/emboss_hmoment.xml" />\n+ <tool file="emboss_5/emboss_iep.xml" />\n+ <tool file="emboss_5/emboss_infoseq.xml" />\n+ <tool file="emboss_5/emboss_isochore.xml" />\n+ <tool file="emboss_5/emboss_lindna.xml" />\n+ <tool file="emboss_5/emboss_marscan.xml" />\n+ <tool file="emboss_5/emboss_maskfeat.xml" />\n+ <tool file="emboss_5/emboss_maskseq.xml" />\n+ <tool file="emboss_5/emboss_matcher.xml" />\n+ <tool file="emboss_5/emboss_megamerger.xml" />\n+ <tool file="emboss_5/emboss_merger.xml" />\n+ <tool file="emboss_5/emboss_msbar.xml" />\n+ <tool file="emboss_5/emboss_needle.xml" />\n+ <tool file="emboss_5/emboss_newcpgreport.xml" /> \n+ <tool file="emboss_5/emboss_newcpgseek.xml" />\n+ <tool file="emboss_5/emboss_newseq.xml" />\n+ <tool file="emboss_5/emboss_noreturn.xml" />\n+ <tool file="emboss_5/emboss_notseq.xml" />\n+ <tool file="emboss_5/emboss_nthseq.xml" />\n+ <tool file="emboss_5/emboss_octanol.xml" />\n+ <tool file="emboss_5/emboss_oddcomp.xml" />\n+ <tool file="emboss_5/emboss_palindrome.xml" />\n+ <tool file="emboss_5/emboss_pasteseq.xml" />\n+ <tool file="emboss_5/emboss_patmatdb.xml" />\n+ <tool file="emboss_5/emboss_pepcoil.xml" />\n+ <tool file="emboss_5/emboss_pepinfo.xml" />\n+ <tool file="emboss_5/emboss_pepnet.xml" />\n+ <tool file="emboss_5/emboss_pepstats.xml" />\n+ <tool file="emboss_5/emboss_pepwheel.xml" />\n+ <tool file="emboss_5/emboss_pepwindow.xml" />\n+ <tool file="emboss_5/emboss_pepwindowall.xml" />\n+ <tool file="emboss_5/emboss_plotcon.xml" />\n+ <tool file="emboss_5/emboss_plotorf.xml" />\n+ <tool file="emboss_5/emboss_polydot.xml" />\n+ <tool file="emboss_5/emboss_preg.xml" />\n+ <tool file="emboss_5/emboss_prettyplot.xml" />\n+ <tool file="emboss_5/emboss_prettyseq.xml" />\n+ <tool file="emboss_5/emboss_primersearch.xml" />\n+ <tool file="emboss_5/emboss_revseq.xml" />\n+ <tool file="emboss_5/emboss_seqmatchall.xml" />\n+ <tool file="emboss_5/emboss_seqret.xml" />\n+ <tool file="emboss_5/emboss_showfeat.xml" /> \n+ <tool file="emboss_5/emboss_shuffleseq.xml" />\n+ <tool file="emboss_5/emboss_sigcleave.xml" />\n+ <tool file="emboss_5/emboss_sirna.xml" />\n+ <tool file="emboss_5/emboss_sixpack.xml" />\n+ <tool file="emboss_5/emboss_skipseq.xml" />\n+ <tool file="emboss_5/emboss_splitter.xml" />\n+ <tool file="emboss_5/emboss_supermatcher.xml" />\n+ <tool file="emboss_5/emboss_syco.xml" />\n+ <tool file="emboss_5/emboss_tcode.xml" />\n+ <tool file="emboss_5/emboss_textsearch.xml" />\n+ <tool file="emboss_5/emboss_tmap.xml" />\n+ <tool file="emboss_5/emboss_tranalign.xml" />\n+ <tool file="emboss_5/emboss_transeq.xml" />\n+ <tool file="emboss_5/emboss_trimest.xml" />\n+ <tool file="emboss_5/emboss_trimseq.xml" />\n+ <tool file="emboss_5/emboss_twofeat.xml" />\n+ <tool file="emboss_5/emboss_union.xml" />\n+ <tool file="emboss_5/emboss_vectorstrip.xml" />\n+ <tool file="emboss_5/emboss_water.xml" />\n+ <tool file="emboss_5/emboss_wobble.xml" />\n+ <tool file="emboss_5/emboss_wordcount.xml" />\n+ <tool file="emboss_5/emboss_wordmatch.xml" /> \n+ </section> \n+-->\n+</toolbox>\n' |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_ancestor_terms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_ancestor_terms.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,62 @@ +<tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.22"> + <description>Collects the ancestor terms from a given term in the given OBO ontology</description> + <command interpreter="perl">/usr/bin/get_ancestor_terms.pl $input_ontology $term_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="term_id" type="text" size="30" value="" label="Term ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <param name="term_id" value="CCO:P0000020"/> + <output name="out_file" file="ancestors.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology. + +**Example** + +If you ask for the descendents of the Gene Ontology term with ID **GO:000800** you will get:: + + GO:0043229 intracellular organelle + GO:0043232 intracellular non-membrane-bounded organelle + GO:0044446 intracellular organelle part + GO:0044424 intracellular part + GO:0005623 cell + GO:0044422 organelle part + GO:0043228 non-membrane-bounded organelle + GO:0044427 chromosomal part + GO:0005575 cellular_component + GO:0000793 condensed chromosome + GO:0043231 intracellular membrane-bounded organelle + GO:0043226 organelle + GO:0005634 nucleus + GO:0044464 cell part + GO:0005622 intracellular + GO:0044454 nuclear chromosome part + GO:0005694 chromosome + GO:0000228 nuclear chromosome + GO:0043227 membrane-bounded organelle + GO:0000794 condensed nuclear chromosome + GO:0000795 synaptonemal complex + GO:0044428 nuclear part + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_child_terms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_child_terms.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,44 @@ +<tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.22"> + <description>Collects the child terms from a given term in the given OBO ontology</description> + <command interpreter="perl">/usr/bin/get_child_terms.pl $input_ontology $term_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="term_id" type="text" size="30" value="" label="Term ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <param name="term_id" value="CCO:P0000020"/> + <output name="out_file" file="children.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Collects the child terms (list of IDs) from a given term (existing ID) in the given OBO ontology. + +**Example** + +If you ask for the children of the Gene Ontology term with ID **GO:0000079** you will get:: + + GO:0031660 regulation of cyclin-dependent protein kinase activity during G2/M + GO:0031657 regulation of cyclin-dependent protein kinase activity during G1/S + GO:0045737 positive regulation of cyclin-dependent protein kinase activity + GO:0045736 negative regulation of cyclin-dependent protein kinase activity + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_descendent_terms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_descendent_terms.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,48 @@ +<tool id="get_descendent_terms" name="Get the descendent terms of a given OBO term" version="1.22"> + <description>Collects the descendent terms from a given term in the given OBO ontology</description> + <command interpreter="perl">/usr/bin/get_descendent_terms.pl $input_ontology $term_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="term_id" type="text" size="30" value="" label="Term ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <param name="term_id" value="CCO:P0000020"/> + <output name="out_file" file="descendents.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Collects the descendent terms (list of IDs) from a given term (existing ID) in the given OBO ontology. + +**Example** + +If you ask for the descendents of the Gene Ontology term with ID **GO:000741** you will get:: + + GO:0048288 nuclear membrane fusion during karyogamy + GO:0000745 nuclear migration during conjugation without cellular fusion + GO:0000744 karyogamy during conjugation without cellular fusion + GO:0032871 regulation of karyogamy + GO:0007344 pronuclear fusion + GO:0000742 karyogamy during conjugation with cellular fusion + GO:0010197 polar nucleus fusion + GO:0000743 nuclear migration during conjugation with cellular fusion + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_intersection_ontology_from.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_intersection_ontology_from.pl Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,27 @@ +#!/usr/bin/perl -w + +use OBO::Parser::OBOParser; +use OBO::Util::Ontolome; + + +use Carp; +use strict; +use warnings; + +my @input_files = @ARGV; + +my $parse_ont = OBO::Parser::OBOParser->new(); +my $ome = OBO::Util::Ontolome->new(); + +my @input_ontos; +foreach(@input_files) +{ + my $onto = $parse_ont->work($_) or warn "ontology not defined, check input files\n"; + push @input_ontos, $onto; +} + +my $intersection_ontology = $ome->intersection(@input_ontos); +$intersection_ontology->export(\*STDOUT, "obo"); + +exit 0; + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_intersection_ontology_from.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_intersection_ontology_from.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,23 @@ +<tool id="get_intersection_ontology_from" name="Gets an intersection ontology from given OBO ontologies" version="1.22"> + <description>Provides an intersection of the given ontologies (in OBO format)</description> + <command interpreter="perl">/usr/bin/get_intersection_ontology_from.pl $input_ontology1 $input_ontology2 > $output</command> + <inputs> + <param format="text" name="input_ontology1" type="data" label="Input Ontology file 1:"/> + <param format="text" name="input_ontology2" type="data" label="Input Ontology file 2:"/> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + +<tests> + <test> + </test> + </tests> + + <help> + +Provides an intersection of the given ontologies (in OBO format) + + </help> + +</tool> |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_list_intersection_from.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_list_intersection_from.pl Tue Jun 07 17:51:45 2011 -0400 |
| [ |
| @@ -0,0 +1,37 @@ +#!/usr/bin/perl -w + +use Carp; +use strict; +use warnings; + +# Takes in first argument +my ($input_file1, $input_file2 ) = @_; + +# Opens the input files + open my $fh, "<", $ARGV[0] or die "could not open $ARGV[0]: $!"; + my @list1 = <$fh>; + + + open my $fh1, "<", $ARGV[1] or die "could not open $ARGV[1]: $!"; + my @list2 = <$fh1>; + +# generates an intersection of terms from the first and second arguments +my @intersection_terms; +foreach (@list1) +{ + my $itemlist1 = $_; + + foreach (@list2) + { + my $itemlist2 = $_; + + if ($itemlist1 eq $itemlist2) + { + push @intersection_terms, $itemlist2; + } + } +} +print @intersection_terms, "\n"; + + +exit 0; |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_list_intersection_from.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_list_intersection_from.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,27 @@ +<tool id="get_list_intersection_from" name="Get the overlapping terms from a given set OBO terms" version="1.22"> + <description>Collects common OBO terms from a given set of list containing OBO terms</description> + <command interpreter="perl">/usr/bin/get_list_intersection_from.pl $input_file1 $input_file2 > $output_file</command> + <inputs> + <param format="tabular" name="input_file1" type="data" label="OBO file 1:"/> + <param format="tabular" name="input_file2" type="data" label="OBO file 2:"/> + </inputs> + <outputs> + <data format="tabular" name="output_file" /> + </outputs> + + <tests> + <test> + <param name="input file 1" value="ancester_terms1.tabular"/> + <param name="input file 2" value="ancester_terms2.tabular"/> + <output name="out_file" file="output_file.tabular"/> + </test> + </tests> + + <help> + +Collects common OBO terms from a given set of lists containing OBO terms. + + </help> + +</tool> + |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_parent_terms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_parent_terms.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,42 @@ +<tool id="get_parent_terms" name="Get the parent terms of a given OBO term" version="1.22"> + <description>Collects the parent terms from a given term in the given OBO ontology</description> + <command interpreter="perl">/usr/bin/get_parent_terms.pl $input_ontology $term_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="term_id" type="text" size="30" value="" label="Term ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <param name="term_id" value="CCO:P0000020"/> + <output name="out_file" file="parents.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Collects the parent terms (list of IDs) from a given term (existing ID) in the given OBO ontology. + +**Example** + +If you ask for the parents of the Gene Ontology term with ID **GO:0000079** you will get:: + + GO:0045859 regulation of protein kinase activity + GO:0051726 regulation of cell cycle + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_relationship_types.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_relationship_types.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,45 @@ +<tool id="get_relationship_types" name="Get all the relationship types in an ontology" version="1.22"> + <description>Collects the relationship types in the given OBO ontology</description> + <command interpreter="perl">/usr/bin/get_relationship_types.pl $input_ontology > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="relationship_types.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + + +Collects all the names of the relationship_types in a given ontology. + +**Example** + +If you ask for the relationships of the Gene Ontology, you will get:: + + is_a + part_of + regulates + has_part + negatively_regulates + positively_regulates + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/get_subontology_from.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/get_subontology_from.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,31 @@ +<tool id="get_subontology_from" name="Get subontology from a given OBO term" version="1.22"> + <description>Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID</description> + <command interpreter="perl">/usr/bin/get_subontology_from.pl $input_ontology $new_root > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="new_root" type="text" size="30" value="" label="Term ID" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + +<tests> + <test> + <param name="input_ontology" value="pre_cco_core.obo"/> + <param name="new_root" value="CCO:P0000003"/> + <output name="output" file="sub_ontology.obo"/> + </test> + </tests> + + <help> + +Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID. + + </help> + +</tool> + + + + + |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/obo2owl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/obo2owl.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,32 @@ +<tool id="obo2owl" name="Convert OBO to OWL" version="1.22"> + <description>Converts an OBO formatted ontology to OWL format</description> + <command interpreter="perl">/usr/bin/obo2owl.pl $input $url $oboinowlurl > $output</command> + <inputs> + <param format="text" name="input" type="data" label="Source file"/> + <param name="url" type="text" size="50" value="http://" label="URL" /> + <param name="oboinowlurl" type="text" size="50" value="http://" label="OBOinOWL URL" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="pre_cco_core.owl"/> + </test> + </tests> + + <help> +This tool transforms an OBO formatted ontology (such as the Gene Ontology) to OWL. + +More information: + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/obo2rdf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/obo2rdf.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,31 @@ +<tool id="obo2rdf" name="Convert OBO to RDF" version="1.22"> + <description>Converts an OBO formatted ontology to RDF/XML format</description> + <command interpreter="perl">/usr/bin/obo2rdf.pl $input $url > $output</command> + <inputs> + <param format="text" name="input" type="data" label="Source file"/> + <param name="url" type="text" size="50" value="http://" label="URL" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="pre_cco_core.rdf"/> + </test> + </tests> + + <help> +This tool transforms an OBO formatted ontology (such as the Gene Ontology) to RDF/XML. + +More information: + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/obo2tran.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/obo2tran.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,31 @@ +<tool id="obo2tran" name="Convert OBO to RDF (tc)" version="1.22"> + <description>Converts an OBO formatted ontology to RDF/XML format with transitive closure</description> + <command interpreter="perl">/usr/bin/obo2tran.pl $input $url > $output</command> + <inputs> + <param format="text" name="input" type="data" label="Source file"/> + <param name="url" type="text" size="50" value="http://" label="URL" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="pre_cco_core_tran.rdf"/> + </test> + </tests> + + <help> +This tool transforms an OBO formatted ontology (such as the Gene Ontology) to an RDF/XML one that has (full) transitive closure. + +More information: + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> + |
| b |
| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/term_id_vs_term_def.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/term_id_vs_term_def.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,46 @@ +<tool id="term_id_vs_term_def" name="Get all the term IDs and term definitions of a given OBO ontology" version="1.22"> + <description>Get all the term IDs and term definitions of a given OBO ontology</description> + <command interpreter="perl">/usr/bin/term_id_vs_term_def.pl $input_ontology > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="term_id_vs_term_name.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Generates a flat file with two columns (TAB separated) with the term_id and term_definition from the elements of the given OBO ontology. + + +**Example** + +If you ask for the term IDs and terms definitions of the Gene Ontology, you will get:: + + GO:0006285 The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired. + GO:0043527 A multimeric protein complex involved in the methylation of specific nucleotides in tRNA. + GO:0005593 Any collagen polymer associated with collagen fibrils and in which the collagen monomers contain two or more relatively short triple-helical domains connected by non-triple-helical sequences; the acronym FACIT stands for fibril-associated collagen with interrupted triple helix. + GO:0015777 The directed movement of teichoic acid into, out of, within or between cells by means of some external agent such as a transporter or pore. Teichoic acid is any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues. + GO:0047104 Catalysis of the reaction: NAD+ + CoA + palmitaldehyde = NADH + palmityl-CoA. + GO:0018302 The incorporation of iron into a 4Fe-4S iron-sulfur cluster via tris-L-cysteinyl-L-N1'-histidino tetrairon tetrasulfide. + ... + ... + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> |
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| diff -r 000000000000 -r 4484575e4186 onto-toolkit/tools/ontology/term_id_vs_term_name.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/onto-toolkit/tools/ontology/term_id_vs_term_name.xml Tue Jun 07 17:51:45 2011 -0400 |
| b |
| @@ -0,0 +1,48 @@ +<tool id="term_id_vs_term_name" name="Get all the term IDs and term names of a given OBO ontology" version="1.22"> + <description>Get all the term IDs and term names of a given OBO ontology</description> + <command interpreter="perl">/usr/bin/term_id_vs_term_name.pl $input_ontology > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco_core.obo"/> + <output name="out_file" file="term_id_vs_term_name.txt"/> + </test> + </tests> + + <help> + +.. class:: infomark + +Generates a flat file with two columns (TAB separated) with the term_id and term_name from the elements of the given OBO ontology. + + +**Example** + +If you ask for the term IDs and terms names of the Gene Ontology, you will get:: + + GO:0050129 N-formylglutamate deformylase activity + GO:0051663 oocyte nucleus localization involved in oocyte dorsal/ventral axis specification + GO:0051712 positive regulation of killing of cells of another organism + GO:0033972 proclavaminate amidinohydrolase activity + GO:0032513 negative regulation of protein phosphatase type 2B activity + GO:0008711 ADP-L-glycero-D-manno-heptose synthase activity + GO:0006285 base-excision repair, AP site formation + GO:0043527 tRNA methyltransferase complex + ... + ... + +**More information** + + ONTO-PERL: An API supporting the development and analysis of bio-ontologies + E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov + Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042 + + </help> + +</tool> |
