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comparison muTect.xml @ 4:7590067ab75d default tip

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made changes
author nilesh
date Wed, 17 Jul 2013 13:21:45 -0500
parents 50a1971f6a7d
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3:50a1971f6a7d 4:7590067ab75d
27 <param name="reference" type="data" format="bed, fasta" label="Select a reference genome"> 27 <param name="reference" type="data" format="bed, fasta" label="Select a reference genome">
28 </param> 28 </param>
29 <param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" /> 29 <param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" />
30 <param name="intervals" type="text" label="Intervals to process" help="In format 'chr1:1500-2500; chr2:2500-3500', separated by semicolons" optional="true"/> 30 <param name="intervals" type="text" label="Intervals to process" help="In format 'chr1:1500-2500; chr2:2500-3500', separated by semicolons" optional="true"/>
31 <param name="intervalfile" type="data" format="txt" label="Intervals to process (.txt file)" help="'chr1:1500-2500', one entry per line" optional="true"/> 31 <param name="intervalfile" type="data" format="txt" label="Intervals to process (.txt file)" help="'chr1:1500-2500', one entry per line" optional="true"/>
32 <param name="normal" type="bam" label="Normal BAM file"/> 32 <param name="normal" type="data" format="bam" label="Normal BAM file"/>
33 <param name="tumor" type="bam" label="Tumor BAM file"/> 33 <param name="tumor" type="data" format="bam" label="Tumor BAM file"/>
34 <conditional name="cosmic"> 34 <conditional name="cosmic">
35 <param name="has_cosmic" type="boolean" label="Cosmic vcf file available for specimen" value="false" /> 35 <param name="has_cosmic" type="boolean" label="Cosmic vcf file available for specimen" value="false" />
36 <when value="true"> 36 <when value="true">
37 <param name="cosmicfile" type="data" format="vcf" label="Cosmic vcf file"/> 37 <param name="cosmicfile" type="data" format="vcf" label="Cosmic vcf file"/>
38 </when> 38 </when>
42 </inputs> 42 </inputs>
43 43
44 <outputs> 44 <outputs>
45 <data format="txt" name="callstats" label="Detailed caller output" from_work_dir="call_stats.txt"/> 45 <data format="txt" name="callstats" label="Detailed caller output" from_work_dir="call_stats.txt"/>
46 <data format="txt" name="coverage" label="Filename for coverage output" from_work_dir="coverage.wig.txt"/> 46 <data format="txt" name="coverage" label="Filename for coverage output" from_work_dir="coverage.wig.txt"/>
47 </data>
48 </outputs> 47 </outputs>
49 48
50 49
51 <help> 50 <help>
52 51