Mercurial > repos > melissacline > ucsc_cancer_utilities

diff segToMatrix.xml @ 52:3a036a34c362

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better handle of input file
author jingchunzhu
date Thu, 17 Sep 2015 15:00:45 -0700
parents 72dc9215623d
children 59dbe857f5d4
line wrap: on
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--- a/segToMatrix.xml	Thu Sep 17 14:33:21 2015 -0700
+++ b/segToMatrix.xml	Thu Sep 17 15:00:45 2015 -0700
@@ -26,11 +26,23 @@
   </outputs>
   <help>
 
-    **Given a segmented copy number data file, convert it into xena ready matrix file.**
+**Given a segmented copy number data file, convert it into xena ready matrix file.**
+
+1. Input data file format: tab-deliminated
 
-    Output File no 1. matrix file
+   =======    =====  ======= ===== ====== ======
+   sanmple    chr    start   end   strand value
+   =======    =====  ======= ===== ====== ======
+   sample1    chr1   1       100   .      0.5
+   sample2    chr1   101     1000  .      1.5
+   sample3    chr1   1000    2000  .      -0.5
+   ...        ...    ...     ...   ...    ...
+   =======    =====  ======= ===== ====== ====== 
 
-    Output File no 2. probeMap file -- probe to gene mapping file  (is in the same genome assembly as the input segmented copy number data)
+
+2. Output File no 1. matrix file
+
+   Output File no 2. probeMap file -- probe to gene mapping file  (is in the same genome assembly as the input segmented copy number data)
   </help>
 </tool>