diff GAFA.xml @ 1:fc8ca4ade638 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 81a1e79dda127d1afc16c7e456bbec16093a3c3f-dirty

--- a/GAFA.xml	Wed Dec 21 07:31:50 2016 -0500
+++ b/GAFA.xml	Mon Feb 20 06:25:33 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="gafa" name="Gene Align and Family Aggregator" version="0.1.0">
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.2.0">
     <description>generates an SQLite database that can be visualised with Aequatus</description>
     <command>
 <![CDATA[
@@ -7,7 +7,7 @@
     -t '$dataset'
 #end for
 #for $dataset in $alignmentFile:
-    -c '$dataset'
+    -a '$dataset'
 #end for
 -g '$genesFile'
 -o '$outputFile'
@@ -15,16 +15,16 @@
     </command>
     <inputs>
         <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
-        <param name="alignmentFile" type="data" format="tabular" multiple="true" label="CDS alignments" help="CDS alignments in tabular format generated by 'T-Coffee to CIGAR' tool" />
-        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get Ensembl features by ID' tool" />
+        <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
+        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get features by Ensembl ID' tool" />
     </inputs>
     <outputs>
         <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
-            <param name="treeFile" ftype="nhx" value="tree.nhx" />
-            <param name="alignmentFile" ftype="tabular" value="cigar.tabular" />
+            <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" />
             <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
         </test>
@@ -35,7 +35,7 @@
 
 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.
 
-N.B.: The tool will modify the sequence identifiers found in the "CDS alignments" dataset by removing everything from the first underscore to the end of the string.
+N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string.
 
 .. _Aequatus: http://aequatus.earlham.ac.uk
 ]]>