diff goslimmer.xml @ 0:d5273661bace draft default tip

Uploaded

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+++ b/goslimmer.xml	Thu May 24 14:01:53 2018 -0400
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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="8.0.112">java-jdk</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal"   description="Fatal ERROR exit code greater than 1" />
+    </stdio>
+	<command interpreter="java -jar">GOSlimmer.jar 
+--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" 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="Mus_musculus_annotations_biomart_e92.tab"/>
+		    <output name="output" ftype="tabular" file="goslim_annotations_mouse.txt" 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/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.
+
+-----
+
+.. 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>