changeset 13:63541ee5f319 draft

Uploaded

--- a/cgatools/tools/cgatools/junctiondiff.xml	Tue Jun 12 13:25:24 2012 -0400
+++ b/cgatools/tools/cgatools/junctiondiff.xml	Tue Jun 12 13:26:06 2012 -0400
@@ -7,16 +7,74 @@
   </requirements>
 
   <command> <!--run executable-->
-  	cgatools junctiondiff --beta -h
+  	cgatools junctiondiff --beta 
+  	--reference $crr.fields.path 
+  	--junctionsA $data_sources.inputA 
+  	--junctionsB $data_sources.inputB 
+  	--scoreThresholdA $scoreA
+  	--scoreThresholdB $scoreB
+  	--distance $distance
+  	--minlength $minlength
+    $stat  
+  	--output-prefix cg_ 
+  	;
+  	mv cg_diff-*tsv cg_diff.tsv
   </command>
 
   <outputs>
-  	<data format="tabular" name="output" />
+  	<data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} on ${on_string}: diff"/>
+		<data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} on ${on_string}: report">
+			<filter>(stat == '--statout')</filter>
+		</data>
   </outputs>
   
   <inputs>
+		<!--form field to select crr file-->
+		<param name="crr" type="select" label="Genome build">
+			<options from_data_table="cg_crr_files" />
+		</param>
+	
+		<!--conditional to select variant file input-->
+  	<conditional name="data_sources">
+      <param name="data_source" type="select" label="Where are the input junction files?">
+        <option value="in" selected="true">imported into Galaxy</option>
+        <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
+      </param>
+      <when value="in">
+				<!--form field to select variant files-->
+				<param name="inputA" type="data" format="tabluar" label="Junction file A">
+					<validator type="unspecified_build" />
+					<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+					 metadata_name="dbkey" metadata_column="1"
+					 message="cgatools is not currently available for this build."/>
+				</param>
+				<param name="inputB" type="data" format="tabluar" label="Junction file B">
+					<validator type="unspecified_build" />
+					<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+					 metadata_name="dbkey" metadata_column="1"
+					 message="cgatools is not currently available for this build."/>
+				</param>
+			</when>
+      <when value="out">
+				<!--form field to enter external input files-->
+				<param name="inputA" type="text" label="Junction file A (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/>
+				<param name="inputB" type="text" label="Junction file B (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/>
+			</when>
+		</conditional>
+		
+		<!--form field to select stats output-->
+		<param name="stat" type="select" label="Print input file stats">
+			<option value="">no</option>
+			<option value="--statout">yes</option>
+		</param>
+
+		<param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
+		<param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
+		<param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
+		<param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500"/>
   </inputs>
 
+
   <help>
   
 **What it does**