comparison goenrichment.xml @ 2:2c7c9646ccf0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit 2983eca17b9a004685024b6f4554a5190d63c7fd

1:5ace5c7d1a86

<tool id="goenrichment" name="GOEnrichment" version="2.0.1">
    <description>performs GO enrichment analysis of a set of gene products</description>
    <requirements>
        <requirement type="package" version="2.0.1">goenrichment</requirement>
    </requirements>
    <command detect_errors="exit_code">goenrichment 
--go '${go}'

--mf_graph '${mf_graph}'
--bp_graph '${bp_graph}'
--cc_graph '${cc_graph}'
    </command>
    <inputs>
        <param name="go" type="data" format="obo,owl" label="Gene Ontology File" help="Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
        <param name="annotation" type="data" format="tabular,txt" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/>
        <param name="study" type="data" format="txt" label="Study Set File" help="File containing the gene products corresponding to the study set (one per line)"/>
        <param name="population" type="data" format="txt" optional="true" label="Population Set File (Optional)" help="File containing the gene products corresponding to the population set (one per line). If no file is submitted, the population set will be the set of all gene products listed in the annotation file."/>
        <param name="correction" type="select" label="Multiple Test Correction" help="The multiple test correction method to use (Benjamini-Hochberg is recommended).">
            <option value="Benjamini-Hochberg" selected="true"/>

.. class:: infomark

GOEnrichment requires:

- A Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
- A tabular annotation file in GAF (http://geneontology.org/page/download-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one.
- A list of gene products comprising the study set (a flat text file with one gene product per line).
- Optionally, a list of gene products comprising the population set (if none is submitted, the population set will be the set of gene products listed in the annotation file).

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2:2c7c9646ccf0

<tool id="goenrichment" name="GOEnrichment" version="2.0.1">
    <description>performs GO enrichment analysis of a set of gene products</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.0.1">goenrichment</requirement>
    </requirements>
    <command detect_errors="exit_code">goenrichment 
--go '${go}'

--mf_graph '${mf_graph}'
--bp_graph '${bp_graph}'
--cc_graph '${cc_graph}'
    </command>
    <inputs>
        <param name="go" type="data" format="obo,owl" label="Gene Ontology File" help="Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@"/>
        <param name="annotation" type="data" format="tabular,txt" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/>
        <param name="study" type="data" format="txt" label="Study Set File" help="File containing the gene products corresponding to the study set (one per line)"/>
        <param name="population" type="data" format="txt" optional="true" label="Population Set File (Optional)" help="File containing the gene products corresponding to the population set (one per line). If no file is submitted, the population set will be the set of all gene products listed in the annotation file."/>
        <param name="correction" type="select" label="Multiple Test Correction" help="The multiple test correction method to use (Benjamini-Hochberg is recommended).">
            <option value="Benjamini-Hochberg" selected="true"/>

.. class:: infomark

GOEnrichment requires:

- A Gene Ontology file in either OBO or OWL format (see @ONTOLOGY_URL@).
- A tabular annotation file in GAF (@ANNOTATION_URL@) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one.
- A list of gene products comprising the study set (a flat text file with one gene product per line).
- Optionally, a list of gene products comprising the population set (if none is submitted, the population set will be the set of gene products listed in the annotation file).

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