diff GAFA.xml @ 4:117fc7414307 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 651fae48371f845578753052c6fe173e3bb35670

--- a/GAFA.xml	Fri Mar 03 07:20:23 2017 -0500
+++ b/GAFA.xml	Wed Mar 15 20:20:58 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="gafa" name="Gene Align and Family Aggregator" version="0.2.0">
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.0">
     <description>generates an SQLite database that can be visualised with Aequatus</description>
     <command>
 <![CDATA[
@@ -16,7 +16,7 @@
     <inputs>
         <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
         <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
-        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get features by Ensembl ID' tool" />
+        <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
     </inputs>
     <outputs>
         <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
@@ -25,7 +25,7 @@
         <test>
             <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" />
             <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" />
-            <param name="genesFile" ftype="json" value="gene.json" />
+            <param name="genesFile" ftype="sqlite" value="gene.sqlite" />
             <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
         </test>
     </tests>