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comparison goslimmer.xml @ 1:de3e053bd6a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit 2983eca17b9a004685024b6f4554a5190d63c7fd
author iuc
date Wed, 24 Jul 2019 05:37:26 -0400
parents 294de027cb5d
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0:294de027cb5d 1:de3e053bd6a5
1 <tool id="goslimmer" name="GOSlimmer" version="1.0.1"> 1 <tool id="goslimmer" name="GOSlimmer" version="1.0.1">
2 <description>converts a set of annotation from GO to a given GOSlim version</description> 2 <description>converts a set of annotation from GO to a given GOSlim version</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.0">goslimmer</requirement> 7 <requirement type="package" version="1.0">goslimmer</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code">goslimmer 9 <command detect_errors="exit_code">goslimmer
7 --go '${go}' 10 --go '${go}'
8 --slim '${slim}' 11 --slim '${slim}'
9 --annotation '${annotation}' 12 --annotation '${annotation}'
10 --output '${output}' 13 --output '${output}'
11 </command> 14 </command>
12 <inputs> 15 <inputs>
13 <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)"/> 16 <param name="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
14 <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)"/> 17 <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
15 <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)"/> 18 <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)"/>
16 </inputs> 19 </inputs>
17 <outputs> 20 <outputs>
18 <data name="output" format="tabular" label="Slim Annotations"/> 21 <data name="output" format="tabular" label="Slim Annotations"/>
19 </outputs> 22 </outputs>
30 33
31 GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version. 34 GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.
32 35
33 It requires: 36 It requires:
34 37
35 - A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology). 38 - A full Gene Ontology file in either OBO or OWL format (see @ONTOLOGY_URL@).
36 - A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide). 39 - A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
37 - 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. 40 - 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.
38 41
39 ----- 42 -----
40 43
41 .. class:: infomark 44 .. class:: infomark
42 45