diff fuma.xml @ 2:76293f7745ff draft

Uploaded

--- a/fuma.xml	Sat Mar 21 03:01:14 2015 -0400
+++ b/fuma.xml	Sun Mar 29 05:28:17 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="fuma" name="FuMa" version="2.6.6.a">
+<tool id="fuma" name="FuMa" version="2.6.6.b">
 	<description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>
 	
 	<requirements>
@@ -36,13 +36,13 @@
 		    $samples_str
 		  -l
 		    $links_str
-		  -f 'list'
+		  -f $output_format
 		  -o $fuma_overview
 	</command>
 	
 	<inputs>
 		<repeat name="datasets" title="FusionGene Datasets" min="2">
-			<param name="sample" type="data" format="txt, tabular" label="Dataset ()" />
+			<param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
 			<param name="format" type="select" label="Format of dataset">
 				<option value="chimerascan">ChimeraScan</option>
 				<option value="defuse">DeFuse</option>
@@ -56,14 +56,48 @@
 				<option value="oncofuse">Oncofuse</option>
 				<option value="trinitygmap">GMAP (As step after Trinity)</option>
 			</param>
-			<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene names if different gene names are being used." />
+			<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />
 		</repeat>
+		
+		<param name="output_format" type="select" label="Output format">
+			<option value="list" selected="true">List</option>
+			<option value="summary">Count summary</option>
+		</param>
 	</inputs>
 	
 	<outputs>
 		<data format="tabular" name="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
 	</outputs>
 	
+	<tests>
+		<test>
+			<!-- <repeat name="datasets"> -->
+				<param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />
+				<param name="datasets_0|format" value="chimerascan" />
+				<param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+			<!-- </repeat> -->
+			<!-- <repeat name="datasets"> -->
+				<param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />
+				<param name="datasets_1|format" value="defuse" />
+				<param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+			<!-- </repeat> -->
+			<!-- <repeat name="datasets"> -->
+				<param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" />
+				<param name="datasets_2|format" value="fusionmap" />
+				<param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+			<!-- </repeat> -->
+			<!-- <repeat name="datasets"> -->
+				<param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" />
+				<param name="datasets_3|format" value="fusionmap" />
+				<param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+			<!-- </repeat> -->
+			
+			<param name="output_format" value="summary" />
+			
+			<output name="fuma_overview" file="output.txt" />
+		</test>
+	</tests>
+	
 	<help>
 	</help>
 </tool>