--- a/velveth.xml	Tue Oct 13 16:38:28 2015 -0400
+++ b/velveth.xml	Wed Feb 12 11:16:32 2020 -0500
@@ -1,24 +1,27 @@
-<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.0">
+<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.1">
   <description>Prepare a dataset for the Velvet velvetg Assembler</description>
-  <version_command>velveth 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <command interpreter="python">
-    velveth_wrapper.py
-           '$out_file1' '$out_file1.extra_files_path'
-           $hash_length
-           $strand_specific
-           #for $i in $inputs
-                ${i.file_format}
-                ${i.read_type}
-                ${i.input}
-           #end for
-  </command>
+  <version_command><![CDATA[
+    velveth 2>&1 | grep "Version" | sed -e 's/Version //'
+  ]]></version_command>
+  <command><![CDATA[
+mkdir -p '${out_file1.extra_files_path}' &&
+velveth
+'${out_file1.extra_files_path}'
+$hash_length
+$strand_specific
+#for $i in $inputs
+    ${i.file_format}
+    ${i.read_type}
+    '${i.input}'
+#end for
+  ]]></command>
   <inputs>
-    <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed.">
+    <param name="hash_length" type="select" label="Hash length" help="k-mer length in base pairs of the words being hashed">
       <option value="11">11</option>
       <option value="13">13</option>
       <option value="15">15</option>
@@ -29,6 +32,87 @@
       <option value="25">25</option>
       <option value="27">27</option>
       <option value="29">29</option>
+      <option value="31">31</option>
+      <option value="33">33</option>
+      <option value="35">35</option>
+      <option value="37">37</option>
+      <option value="39">39</option>
+      <option value="41">41</option>
+      <option value="43">43</option>
+      <option value="45">45</option>
+      <option value="47">47</option>
+      <option value="49">49</option>
+      <option value="51">51</option>
+      <option value="53">53</option>
+      <option value="55">55</option>
+      <option value="57">57</option>
+      <option value="59">59</option>
+      <option value="61">61</option>
+      <option value="63">63</option>
+      <option value="65">65</option>
+      <option value="67">67</option>
+      <option value="69">69</option>
+      <option value="71">71</option>
+      <option value="73">73</option>
+      <option value="75">75</option>
+      <option value="77">77</option>
+      <option value="79">79</option>
+      <option value="81">81</option>
+      <option value="83">83</option>
+      <option value="85">85</option>
+      <option value="87">87</option>
+      <option value="89">89</option>
+      <option value="91">91</option>
+      <option value="93">93</option>
+      <option value="95">95</option>
+      <option value="97">97</option>
+      <option value="99">99</option>
+      <option value="101">101</option>
+      <option value="103">103</option>
+      <option value="105">105</option>
+      <option value="107">107</option>
+      <option value="109">109</option>
+      <option value="111">111</option>
+      <option value="113">113</option>
+      <option value="115">115</option>
+      <option value="117">117</option>
+      <option value="119">119</option>
+      <option value="121">121</option>
+      <option value="123">123</option>
+      <option value="125">125</option>
+      <option value="127">127</option>
+      <option value="129">129</option>
+      <option value="131">131</option>
+      <option value="133">133</option>
+      <option value="135">135</option>
+      <option value="137">137</option>
+      <option value="139">139</option>
+      <option value="141">141</option>
+      <option value="143">143</option>
+      <option value="145">145</option>
+      <option value="147">147</option>
+      <option value="149">149</option>
+      <option value="151">151</option>
+      <option value="153">153</option>
+      <option value="155">155</option>
+      <option value="157">157</option>
+      <option value="159">159</option>
+      <option value="161">161</option>
+      <option value="163">163</option>
+      <option value="165">165</option>
+      <option value="167">167</option>
+      <option value="169">169</option>
+      <option value="171">171</option>
+      <option value="173">173</option>
+      <option value="175">175</option>
+      <option value="177">177</option>
+      <option value="179">179</option>
+      <option value="181">181</option>
+      <option value="183">183</option>
+      <option value="185">185</option>
+      <option value="187">187</option>
+      <option value="189">189</option>
+      <option value="191">191</option>
     </param>
     <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/>
     <repeat name="inputs" title="Input Files">
@@ -51,11 +135,8 @@
     </repeat>
   </inputs>
   <outputs>
-    <data format="velvet" name="out_file1" />
+    <data name="out_file1" format="velvet" />
   </outputs>
-  <requirements>
-    <requirement type="package">velvet</requirement>
-  </requirements>
   <tests>
     <test>
       <param name="hash_length" value="21" />
@@ -67,13 +148,12 @@
       <!-- </repeat> -->
       <param name="strand_specific" value="" />
       <output name="out_file1" file="velveth_test1/output.html" lines_diff="4">
-        <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" />
-        <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" />
+        <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
+        <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
       </output>
     </test>
   </tests>
-  <help>
-
+  <help><![CDATA[
 **What it does**
 
 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
@@ -130,7 +210,6 @@
   shortPaired2 (see above)
   long (for Sanger, 454 or even reference sequences)
   longPaired
-
-  </help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>