# HG changeset patch
# User Rayan Chikhi <chikhi@psu.edu>
# Date 1375819785 14400
# Node ID f7796b819c622040af56b6ac0542761364117a3c
# Parent  3c8d8ebb7d1b07005db1b6f39e01f552ecbbd78a
fixed xml

diff -r 3c8d8ebb7d1b -r f7796b819c62 kmergenie.xml
--- a/kmergenie.xml	Tue Aug 06 13:48:34 2013 -0400
+++ b/kmergenie.xml	Tue Aug 06 16:09:45 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool id="kmergenie" name="KmerGenie" version="1.5626">
   <description>k-mer histograms analysis</description>
-  <requirements><requirement type="package">kmergenie</requirement></requirements>
+  <requirements><requirement type="package" version="1.5626">kmergenie</requirement></requirements>
   <command interpreter="python">
      ## assumes that kmergenie folder is in $PATH, my install doesn't use tool_dependency_dir yet
      stderr_wrapper.py kmergenie $input
@@ -12,6 +12,14 @@
         #if $params.l != '':
             -l $params.l
         #end if
+        #if $params.s != '':
+            -s $params.s
+        #end if
+        #if $params.sampling_mode.type_select == 'manual':
+            -e $params.sampling_mode.e
+        #end if
+        $params.two_passes
+        $params.use_diploid
      #end if
      -o ${html_file.files_path}/kmergenie_$input.name
      1> /dev/null 
@@ -41,7 +49,7 @@
           <when value="autodetect">
                 </when>
         </conditional>
-        <param name="one_pass" type="boolean" label="Precise estimation of k" truevalue="--one-pass" falsevalue="" checked="True" help="Performs a second pass to find the optimal k value within 2 bp" />
+        <param name="two_passes" type="boolean" label="Precise estimation of k" truevalue="" falsevalue="--one-pass" checked="True" help="Performs a second pass to find the optimal k value within 2 bp" />
         <param name="use_diploid" type="boolean" label="Diploid organism" help="" truevalue="--diploid" falsevalue="" checked="False"/>
       </when>
       <when value="autodetect">
@@ -60,7 +68,7 @@
   </stdio>
   <tests>
     <test>
-      <param name="input_file" value="1000gsample.fastq" />
+      <param name="input" ftype="fastq" value="1000gsample.fastq" />
       <param name="type_select" value="autodetect"/>
       <output name="html_file" file="kmergenie_report.html" ftype="html" lines_diff="1"/>
     </test>