diff find_intervals.xml @ 21:d6b961721037

Miller Lab Devshed version 4c04e35b18f6

--- a/find_intervals.xml	Tue Oct 23 14:38:04 2012 -0400
+++ b/find_intervals.xml	Mon Nov 05 12:44:17 2012 -0500
@@ -22,41 +22,41 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="tabular" label="Input">
+    <param name="input" type="data" format="tabular" label="Dataset">
       <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
     </param>
 
     <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
 
     <conditional name="cutoff">
-      <param name="type" type="select" label="Cutoff type">
+      <param name="type" type="select" label="Score-shift type">
         <option value="percentage">percentage</option>
         <option value="value">value</option>
       </param>
       <when value="percentage">
-        <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/>
+        <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage score-shift"/>
       </when>
       <when value="value">
-        <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/>
+        <param name="cutoff_val" type="float" value="0.0" label="Value score-shift"/>
       </when>
     </conditional>
 
     <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
 
     <param name="out_format" type="select" format="integer" label="Report individual positions">
-      <option value="0" selected="true">No</option>
-      <option value="1">Yes</option>
+      <option value="0" selected="true">no</option>
+      <option value="1">yes</option>
     </param>
 
     <conditional name="override_metadata">
-      <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you need to choose the columns if the input dataset is not gd_snp">
-        <option value="0" selected="true">No, get columns from metadata</option>
-        <option value="1" >Yes, choose columns</option>
+      <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you must choose the columns if the input dataset is not gd_snp.">
+        <option value="0" selected="true">no, get columns from metadata</option>
+        <option value="1" >yes, choose columns here</option>
       </param>
       <when value="0" />
       <when value="1">
-        <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure the build in the metadata is the same as using here."/>
-        <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero or one based positions will work"/>
+        <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure this corresponds to the build recorded in the metadata."/>
+        <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero-based or one-based positions will work."/>
       </when>
     </conditional>
   </inputs>
@@ -105,14 +105,14 @@
 For gd_snp format the metadata can be used to specify the chromosome and 
 position.
 Other inputs include
-a percentage or raw score for the "cutoff" which should be greater than the 
+a percentage or raw score for the "score-shift" which should be greater than the 
 average value for the scores column.  A higher value will give smaller intervals
 in the output.
 If a percentage (e.g. 95%) is specified
-then that percentile of the scores is used as the cutoff; 
+then that percentile of the scores is used as the shift; 
 percentile may not work well if many rows or SNPs have the same score
 (in that case use a raw score).  The program subtracts the
-cutoff from every score, then finds genomic intervals (i.e., consecutive runs
+shift from every score, then finds genomic intervals (i.e., consecutive runs
 of SNPs) whose total score cannot be increased by adding or subtracting one
 or more adjusted scores at the ends of the interval.
 Another input is the number of times the