# HG changeset patch
# User bonsai
# Date 1379084322 14400
# Node ID 87874e4511beab4f3451354eeacb4324f6191a2a
# Parent  9fe9c48f59704398afaf4b4ef9929a73c170fb33
Uploaded

diff -r 9fe9c48f5970 -r 87874e4511be crac.xml
--- a/crac.xml	Fri Sep 13 10:47:23 2013 -0400
+++ b/crac.xml	Fri Sep 13 10:58:42 2013 -0400
@@ -10,9 +10,7 @@
               #else
    <!--1-->      "$Genome.index_input.extra_files_path"
               #end if
-              #if $condi_compressed == "yes"
-                --gz
-              #end if
+              $compressed
    <!--2-->   $output_name.extra_files_path		<!-- Usefull for submitting jobs on crac.sh-->
               -r $input -k $kmer_length --read-length $read_length --sam $output_name
               #if $condi_deep_snp.deepSNP == "yes"
@@ -30,9 +28,7 @@
                 --min-support-no-cover $choixSettings.min_support_no_cover
                 --min-break-length $choixSettings.min_break_length
               #end if
-              #if str($detailed_sam) == "yes"
-                --detailed-sam 
-              #end if
+              $detailed_sam
               
    </command>
 
@@ -60,20 +56,21 @@
       </conditional>
 
 
-      <param name="input" format="txt,raw,fastq" type="data" label="Reads File" help="Select a file"/>   
+      <param name="input" format="txt,raw,fasta,fastq" type="data" label="Reads file" help="Select a file"/>   
       <param name="kmer_length" type="integer" min="12" max="32" value="22" label="k-mer length"> 
          <help>k-mer length must be carefully chosen. A k-mer of that length must map to a unique location in the genome with a high probability. Recommended value for the human genome: 22</help>  
       </param> 
-      <param name="read_length" type="integer" label="Read length" value="0" help="Set read length when all reads have the same length to dramatically increase computation speed. Default value (no read length considered) : 0. Note : If read length is set, shorter reads will be ignored, longer reads will be cut."/>
-      <param name="detailed_sam" type="select" label="Do you want a detailed sam output file ?" help="Detailed sam output file gives you information on the SNPs, splice junctions, sequencing errors, chimeras, ..." >
-         <option value="no"> No, I don't want a detailed SAM output file </option>
-         <option value="yes"> Yes, I want a detailed SAM output file </option>
-         <when value="yes"/>				<!-- Supress warnings-->
-         <when value="no"/>				<!-- Supress warnings-->
+      <param name="read_length" type="integer" label="Read length" value="0" 
+             help="When all reads have the same length, set the read length to dramatically increase computation speed. 
+                   Default value (no read length considered): 0. 
+                   Note : If read length is set, shorter reads will be ignored, longer reads will be cut."/>
+      <param name="detailed_sam" type="select" format="text" label="Do you want a detailed sam output file ?" help="Detailed sam output file gives you information on the SNPs, splice junctions, sequencing errors, chimeras, ..." >
+         <option value=""> No, I don't want a detailed SAM output file </option>
+         <option value="--detailed-sam"> Yes, I want a detailed SAM output file </option>
       </param>
-      <param name="condi_compressed" type="select" display="radio" label="Compress output files?">
-        <option value="yes">Yes</option>
-        <option value="no">No</option>
+      <param name="compressed" type="select" display="radio" label="Compress output files?">
+        <option value="" selected="true">No</option>
+        <option value="--gz">Yes</option>
       </param>
       <conditional name="condi_deep_snp">		<!-- Conditional 1 -->
 		<param type="select" name="deepSNP" label="Search hard for SNPs?">