--- a/velvetg.xml	Wed Feb 12 11:16:32 2020 -0500
+++ b/velvetg.xml	Tue Jun 16 12:58:20 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1">
+<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.2">
   <description>Velvet sequence assembler for very short reads</description>
   <macros>
     <import>macros.xml</import>
@@ -9,102 +9,85 @@
     velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
   ]]></version_command>
   <command><![CDATA[
-ln -s '$input.extra_files_path'/Roadmaps &&
-ln -s '$input.extra_files_path'/Sequences &&
-velvetg .
-#if $generate_amos.afg  == "yes":
-    -amos_file $generate_amos.afg
-#end if
-#if $unused_reads.generate_unused  == "yes":
-    -unused_reads $unused_reads.generate_unused
-#end if
-$read_trkg
-#if $coverage.cutoff == "auto":
-    -cov_cutoff auto
-#elif $coverage.cutoff == "value":
-    -cov_cutoff $coverage.cov_cutoff
-#end if
-#if $expected.coverage == "auto":
-    -exp_cov auto
-#elif $expected.coverage == "value":
-    -exp_cov $expected.exp_cov
-#end if
-#if $contig_lgth.use_contig_lgth == "yes":
-    -min_contig_lgth $contig_lgth.min_contig_lgth
-#end if
-#if $reads.paired == "yes":
-    #if int($reads.ins_length) > 0:
-        -ins_length $reads.ins_length
-    #end if
-    #if $reads.options.advanced == "yes":
-        #if int($reads.options.ins_length_sd) > 0:
-            -ins_length_sd $reads.options.ins_length_sd
-        #end if
-        #if int($reads.options.ins_length2) > 0:
-            -ins_length2 $reads.options.ins_length2
-        #end if
-        #if int($reads.options.ins_length2_sd) > 0:
-            -ins_length2_sd $reads.options.ins_length2_sd
-        #end if
-        #if int($reads.options.ins_length_long) > 0:
-            -ins_length_long $reads.options.ins_length_long
-        #end if
-        #if int($reads.options.ins_length_long_sd) > 0:
-            -ins_length_long_sd $reads.options.ins_length_long_sd
-        #end if
-        #if int($reads.options.max_branch_length) > 0:
-            -max_branch_length $reads.options.max_branch_length
-        #end if
-        #if int($reads.options.max_divergence) > 0:
-            -max_divergence $reads.options.max_divergence
-        #end if
-        #if int($reads.options.max_gap_count) > 0:
-            -max_gap_count $reads.options.max_gap_count
-        #end if
-        #if int($reads.options.min_pair_count) > 0:
-            -min_pair_count $reads.options.min_pair_count
-        #end if
-        #if int($reads.options.max_coverage) > 0:
-            -max_coverage $reads.options.max_coverage
-        #end if
-        #if int($reads.options.long_mult_cutoff) > 0:
-            -long_mult_cutoff $reads.options.long_mult_cutoff
-        #end if
-        $reads.options.scaffolding
-    #end if
-#end if
+    ln -s '$input.extra_files_path'/Roadmaps &&
+    ln -s '$input.extra_files_path'/Sequences &&
+    velvetg .
+           #if 'amos' in $add_out:
+               -amos_file yes
+           #end if
+           #if 'unused' in $add_out:
+               -unused_reads yes
+           #end if
+           $read_trkg
+           #if $coverage.cutoff == "auto":
+               -cov_cutoff auto
+           #elif $coverage.cutoff == "value":
+               -cov_cutoff $coverage.cov_cutoff
+           #end if
+           #if $expected.coverage == "auto":
+               -exp_cov auto
+           #elif $expected.coverage == "value":
+               -exp_cov $expected.exp_cov
+           #end if
+           #if $contig_lgth.use_contig_lgth == "yes":
+               -min_contig_lgth $contig_lgth.min_contig_lgth
+           #end if
+           #if $reads.paired == "yes":
+               #if int($reads.ins_length) > 0:
+                   -ins_length $reads.ins_length
+               #end if
+               #if $reads.options.advanced == "yes":
+                   #if int($reads.options.ins_length_sd) > 0:
+                       -ins_length_sd $reads.options.ins_length_sd
+                   #end if
+                   #if int($reads.options.ins_length2) > 0:
+                       -ins_length2 $reads.options.ins_length2
+                   #end if
+                   #if int($reads.options.ins_length2_sd) > 0:
+                       -ins_length2_sd $reads.options.ins_length2_sd
+                   #end if
+                   #if int($reads.options.ins_length3) > 0:
+                       -ins_length3 $reads.options.ins_length3
+                   #end if
+                   #if int($reads.options.ins_length3_sd) > 0:
+                       -ins_length3_sd $reads.options.ins_length3_sd
+                   #end if
+                   #if int($reads.options.ins_length4) > 0:
+                       -ins_length4 $reads.options.ins_length4
+                   #end if
+                   #if int($reads.options.ins_length4_sd) > 0:
+                       -ins_length4_sd $reads.options.ins_length4_sd
+                   #end if
+                   #if int($reads.options.ins_length_long) > 0:
+                       -ins_length_long $reads.options.ins_length_long
+                   #end if
+                   #if int($reads.options.ins_length_long_sd) > 0:
+                       -ins_length_long_sd $reads.options.ins_length_long_sd
+                   #end if
+                   #if int($reads.options.max_branch_length) > 0:
+                       -max_branch_length $reads.options.max_branch_length
+                   #end if
+                   #if int($reads.options.max_divergence) > 0:
+                       -max_divergence $reads.options.max_divergence
+                   #end if
+                   #if int($reads.options.max_gap_count) > 0:
+                       -max_gap_count $reads.options.max_gap_count
+                   #end if
+                   #if int($reads.options.min_pair_count) > 0:
+                       -min_pair_count $reads.options.min_pair_count
+                   #end if
+                   #if int($reads.options.max_coverage) > 0:
+                       -max_coverage $reads.options.max_coverage
+                   #end if
+                   #if int($reads.options.long_mult_cutoff) > 0:
+                       -long_mult_cutoff $reads.options.long_mult_cutoff
+                   #end if
+                   $reads.options.scaffolding
+               #end if
+           #end if
   ]]></command>
   <inputs>
     <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
-    <conditional name="generate_amos">
-      <param name="afg" type="select" label="Generate a AMOS.afg file">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-      </param>
-      <when value="no"/>
-      <when value="yes"/>
-    </conditional>
-
-    <conditional name="unused_reads">
-      <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-      </param>
-      <when value="no"/>
-      <when value="yes"/>
-    </conditional>
-
-    <conditional name="last_graph">
-      <param name="generate_graph" type="select" label="Generate velvet LastGraph file">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-      </param>
-      <when value="no"/>
-      <when value="yes"/>
-    </conditional>
-
-    <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
-
     <conditional name="coverage">
       <param name="cutoff" type="select" label="Coverage cutoff" help="">
         <option value="none">None</option>
@@ -117,7 +100,17 @@
         <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
       </when>
     </conditional>
-
+    <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
+    <conditional name="contig_lgth">
+      <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
+        <option value="no">No</option>
+        <option value="yes">Yes</option>
+      </param>
+      <when value="no"/>
+      <when value="yes">
+        <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
+      </when>
+    </conditional>
     <conditional name="expected">
       <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
         <option value="none">None</option>
@@ -131,16 +124,11 @@
       </when>
     </conditional>
 
-    <conditional name="contig_lgth">
-      <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-      </param>
-      <when value="no"/>
-      <when value="yes">
-        <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
-      </when>
-    </conditional>
+    <param name="add_out" type="select" multiple="true" optional="true" label="Additional outputs" help="">
+        <option value="amos">Generate a AMOS.afg file</option>
+        <option value="unused">Generate a UnusedReads fasta file</option>
+        <option value="lastgraph">Generate velvet LastGraph file</option>
+    </param>
 
     <conditional name="reads">
       <param name="paired" type="select" label="Using Paired Reads">
@@ -160,6 +148,10 @@
             <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
             <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
             <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
+            <param name="ins_length3" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
+            <param name="ins_length3_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
+            <param name="ins_length4" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
+            <param name="ins_length4_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
             <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
             <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
             <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
@@ -169,50 +161,53 @@
             <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
             <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
             <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>
-
           </when>
         </conditional>
       </when>
     </conditional>
+<!-- TODO
+-coverage_mask
+-paired_exp_fraction
+-alignments
+-exportFiltered
+-clean
+-very_clean
+-shortMatePaired-->
   </inputs>
   <outputs>
     <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
       <filter>read_trkg is True</filter>
     </data>
     <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
-      <filter>last_graph['generate_graph'] == "yes"</filter>
+      <filter>'lastgraph' in add_out</filter>
     </data>
     <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
-      <filter>generate_amos['afg'] == "yes"</filter>
+      <filter>'amos' in add_out</filter>
     </data>
     <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
-      <filter>unused_reads['generate_unused'] == "yes"</filter>
+      <filter>'unused' in add_out</filter>
     </data>
     <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
     <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
   </outputs>
   <tests>
-    <test>
-      <param name="input" value="velveth_test1/output.html" ftype="velvet">
-        <composite_data value="velveth_test1/Sequences" />
-        <composite_data value="velveth_test1/Roadmaps" />
-        <composite_data value="velveth_test1/Log"/>
+    <test expect_num_outputs="5">
+      <param name="input" value="velvetg_paired.out" ftype="velvet" >
+        <composite_data value='velvetg_paired/Sequences'/>
+        <composite_data value='velvetg_paired/Roadmaps'/>
+        <composite_data value='velvetg_paired/Log'/>
       </param>
-      <param name="afg" value="yes" />
-      <param name="generate_unused" value="yes" />
-      <param name="generate_graph" value="no" />
+      <param name="add_out" value="amos,unused,lastgraph" />
       <param name="read_trkg" value="-read_trkg no" />
       <param name="cutoff" value="auto" />
       <param name="coverage" value="auto" />
       <param name="use_contig_lgth" value="no" />
       <param name="paired" value="no" />
-      <!--
-      <output name="LastGraph" file="velvetg_test1/lastgraph.txt"/>
-      -->
-      <output name="velvet_asm" file="velvetg_test1/amos.afg" />
-      <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" />
-      <output name="stats" file="velvetg_test1/stats.csv" />
-      <output name="contigs" file="velvetg_test1/contigs.fa" />
+      <output name="velvet_asm" file="velvetg_paired/velvet_asm.afg" compare="diff"/>
+      <output name="unused_reads_fasta" file="velvetg_paired/UnusedReads.fa" compare="diff"/>
+      <output name="LastGraph" file="velvetg_paired/lastgraph.txt" compare="diff"/>
+      <output name="stats" file="velvetg_paired/stats.txt" compare="diff"/>
+      <output name="contigs" file="velvetg_paired/contigs.fa" compare="diff"/>
     </test>
   </tests>
   <help><![CDATA[