diff goslimmer.xml @ 0:294de027cb5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb

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+<tool id="goslimmer" name="GOSlimmer" version="1.0.1">
+    <description>converts a set of annotation from GO to a given GOSlim version</description>
+    <requirements>
+        <requirement type="package" version="1.0">goslimmer</requirement>
+    </requirements>
+    <command detect_errors="exit_code">goslimmer 
+--go '${go}'
+--slim '${slim}'
+--annotation '${annotation}'
+--output '${output}'
+    </command>
+    <inputs>
+        <param name="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
+        <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim 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)"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="Slim Annotations"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="go" ftype="obo" value="go.obo"/>
+            <param name="slim" ftype="obo" value="goslim_generic.obo"/>
+            <param name="annotation" ftype="txt" value="annotations.tab"/>
+            <output name="output" ftype="tabular" file="slim_annotations.tab" lines_diff="0"/>
+        </test>
+    </tests>
+    <help>
+.. class:: infomark
+
+GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.
+
+It requires:
+
+- A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
+- A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
+- 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.
+
+-----
+
+.. class:: infomark
+
+GOSlimmer can also be applied to other pairs of OWL/OBO ontologies where one is a subset of the other and you want to convert annotations from the larger to the smaller one.
+    </help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubgoslimmer,
+  author = {Faria, Daniel},
+  year = {2017},
+  title = {GOSlimmer},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/DanFaria/GOSlimmer},
+}
+        </citation>
+    </citations>
+</tool>