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changeset 1:ae2bc4e5fefc draft default tip

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Fix igvtools_tile.xml tdf output and add log file output
author Jim Johnson <jj@umn.edu>
date Tue, 27 Nov 2012 16:32:10 -0600
parents 2eb1e2924c1a
children
files igvtools_tile.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/igvtools_tile.xml	Tue Jan 17 21:53:25 2012 -0500
+++ b/igvtools_tile.xml	Tue Nov 27 16:32:10 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="igvtools_tile" name="IGVtools tile" version="1.0">
+<tool id="igvtools_tile" name="IGVtools tile" version="1.1">
   <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
   <command interpreter="bash">igvtools tile 
     #if $zoom.__str__ != '':
@@ -22,7 +22,7 @@
     #elif $input.datatype.file_ext == 'igv':
        #set $input_name='input_file.igv'
     #end if
-    `ln -s $input  $input_name; echo $input_name` $output_tdf $refGenomeSource.ref
+    `ln -s $input  $input_name; echo $input_name` output.tdf $refGenomeSource.ref 1> igv.stdout
   </command>
   <inputs>
     <conditional name="refGenomeSource">
@@ -64,6 +64,7 @@
   </inputs>
   <outputs>
     <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
+    <data format="txt" name="logfile" metadata_source="input" label="${tool.name} on ${on_string}: igv.log" from_work_dir="igv.stdout"/>
   </outputs>
   <tests>
   </tests>