diff gemini_windower.xml @ 5:3b5b1ebc8423 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

--- a/gemini_windower.xml	Fri Dec 14 12:41:48 2018 -0500
+++ b/gemini_windower.xml	Fri Jan 11 17:38:04 2019 -0500
@@ -1,5 +1,5 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
-    <description>Conducting analyses on genome "windows"</description>
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
+    <description>Compute sliding window statistics from variants</description>
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">windower</token>
@@ -14,19 +14,21 @@
             -s $s
             -t $window_analysis
             -o $operation
-            "${ infile }"
-            > "${ outfile }"
+            '$infile'
+            > '$outfile'
 ]]>
     </command>
     <inputs>
         <expand macro="infile" />
 
-        <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
+        <param argument="-t" name="window_analysis" type="select"
+        label="The type of window analysis requested?" help="">
             <option value="nucl_div">(nucl_div)</option>
             <option value="hwe">(hwe)</option>
         </param>
 
-        <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
+        <param argument="-o" name="operation" type="select"
+        label="The operation that should be applied to the -t values" help="">
             <option value="mean">mean</option>
             <option value="median">median</option>
             <option value="min">min</option>
@@ -34,18 +36,11 @@
             <option value="collapse">collapse</option>
         </param>
 
-        <param name="w" type="integer" value="10000" label="The window size in bp"
-            help="(-w)">
-            <validator type="in_range" min="0"/>
-        </param>
-
-        <param name="s" type="integer" value="1000" label="The step size for the windows in bp"
-            help="(-s)">
-            <validator type="in_range" min="0"/>
-        </param>
-
+        <param argument="-w" name="w" type="integer" value="10000" min="2"
+        label="Window size in bp" help="" />
+        <param argument="-s" name="s" type="integer" value="1000" min="0"
+        label="Step size for sliding the window in bp" help="Specify 0 here for sliding by one full window size" />
     </inputs>
-
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
@@ -62,27 +57,28 @@
     <help><![CDATA[
 **What it does**
 
-It computs variation metrics across genomic windows (both fixed and sliding).
+Compute variation metrics across genomic windows.
 
 **Examples**
 
-Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
+Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows::
 
  -w 50000 
  -s 0 
  -t nucl_div 
  -o mean
 
-Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
+Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb::
 
  -w 50000
  -s 10000
  -t nucl_div
  -o mean 
 
-Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
+Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome::
 
- -w 10000 
+ -w 10000
+ -s 100000
  -t hwe
  -o max