Mercurial > repos > iuc > goslimmer

changeset 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
children
files goslimmer.xml macros.xml
diffstat 2 files changed, 11 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/goslimmer.xml	Fri Jan 11 06:18:00 2019 -0500
+++ b/goslimmer.xml	Wed Jul 24 05:37:26 2019 -0400
@@ -1,5 +1,8 @@
 <tool id="goslimmer" name="GOSlimmer" version="1.0.1">
     <description>converts a set of annotation from GO to a given GOSlim version</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="1.0">goslimmer</requirement>
     </requirements>
@@ -10,8 +13,8 @@
 --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="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
+        <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim 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)"/>
     </inputs>
     <outputs>
@@ -32,9 +35,9 @@
 
 It requires:
 
-- A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
+- A full Gene Ontology file in either OBO or OWL format (see @ONTOLOGY_URL@).
 - 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.
+- 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.
 
 -----
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jul 24 05:37:26 2019 -0400
@@ -0,0 +1,4 @@
+<tokens>
+    <token name="@ANNOTATION_URL@">http://geneontology.org/docs/download-go-annotations</token>
+    <token name="@ONTOLOGY_URL@">http://geneontology.org/docs/download-ontology</token>
+</tokens>