diff macs2_bdgcmp.xml @ 20:f63ccb331626 draft

Uploaded

--- a/macs2_bdgcmp.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/macs2_bdgcmp.xml	Thu May 01 17:07:46 2014 -0400
@@ -19,18 +19,18 @@
     </command>
     <expand macro="stdio" />
     <inputs>
+        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
         <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />
-        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
 
         <conditional name="bdgcmp_options">
             <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value">
                 <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
                 <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
                 <option value="subtract">subtraction from treatment (subtract)</option>
-                <option value="logFE">log10 fold enrichment (logFR)</option>
+                <option value="logFE">log10 fold enrichment (logFE)</option>
                 <option value="FE">linear scale fold enrichment (FE)</option>
                 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
-                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models and open chromatin model (slogLR)</option>
+                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
             </param>
             <when value="FE">
                 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>