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comparison igvtools_tile.xml @ 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
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equal deleted inserted replaced
0:2eb1e2924c1a 1:ae2bc4e5fefc
1 <tool id="igvtools_tile" name="IGVtools tile" version="1.0"> 1 <tool id="igvtools_tile" name="IGVtools tile" version="1.1">
2 <description>convert a sorted data input file to a binary tiled data (.tdf) file</description> 2 <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
3 <command interpreter="bash">igvtools tile 3 <command interpreter="bash">igvtools tile
4 #if $zoom.__str__ != '': 4 #if $zoom.__str__ != '':
5 -z $zoom 5 -z $zoom
6 #end if 6 #end if
20 #elif $input.datatype.file_ext == 'igv.cn': 20 #elif $input.datatype.file_ext == 'igv.cn':
21 #set $input_name='input_file.cn' 21 #set $input_name='input_file.cn'
22 #elif $input.datatype.file_ext == 'igv': 22 #elif $input.datatype.file_ext == 'igv':
23 #set $input_name='input_file.igv' 23 #set $input_name='input_file.igv'
24 #end if 24 #end if
25 `ln -s $input $input_name; echo $input_name` $output_tdf $refGenomeSource.ref 25 `ln -s $input $input_name; echo $input_name` output.tdf $refGenomeSource.ref 1> igv.stdout
26 </command> 26 </command>
27 <inputs> 27 <inputs>
28 <conditional name="refGenomeSource"> 28 <conditional name="refGenomeSource">
29 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?"> 29 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
30 <option value="built-in">Use a built-in reference</option> 30 <option value="built-in">Use a built-in reference</option>
62 chr start end name 62 chr start end name
63 where name is the probe name in the .gct file."/> 63 where name is the probe name in the .gct file."/>
64 </inputs> 64 </inputs>
65 <outputs> 65 <outputs>
66 <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/> 66 <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
67 <data format="txt" name="logfile" metadata_source="input" label="${tool.name} on ${on_string}: igv.log" from_work_dir="igv.stdout"/>
67 </outputs> 68 </outputs>
68 <tests> 69 <tests>
69 </tests> 70 </tests>
70 <help> 71 <help>
71 **What it does** 72 **What it does**