# HG changeset patch
# User ulfschaefer
# Date 1466073613 14400
# Node ID f05fa489089bd6b31b12fdfb510a52e4da1ff35d
# Parent  29a682a7dd16b685802a1631f2993baa02c892ac
Uploaded

diff -r 29a682a7dd16 -r f05fa489089b vcfs2fasta.xml
--- a/vcfs2fasta.xml	Thu Jun 16 06:40:02 2016 -0400
+++ b/vcfs2fasta.xml	Thu Jun 16 06:40:13 2016 -0400
@@ -17,98 +17,140 @@
   </stdio>
   <command interpreter="bash">
     vcfs2fasta.sh
-	$output
-	#if str($mix_cond.mix) == "yes":
+    $output
+    #if str($mix_cond.mix) == "yes":
         $mix_cond.mix_value
     #else
         NOTTHERE
     #end if
-	#if str($cols_cond.cols) == "yes":
-        $cols_cond.column_ns
+    #if str($coln_cond.coln) == "yes":
+        $coln_cond.column_ns
     #else
         NOTTHERE
     #end if
-	#if str($sample_cond.sample) == "yes":
-        $sample_cond.sample_ns
+    #if str($colgap_cond.colgap) == "yes":
+        $colgap_cond.column_ns
+    #else
+        NOTTHERE
+    #end if
+    #if str($samplen_cond.samplen) == "yes":
+        $samplen_cond.sample_ns
+    #else
+        NOTTHERE
+    #end if
+    #if str($samplegap_cond.samplegap) == "yes":
+        $samplegap_cond.sample_gaps
     #else
         NOTTHERE
     #end if
-	#if str($reference_cond.reference) == "yes":
-		$reference_cond.ref_fa
-	#else
+    #if str($reference_cond.reference) == "yes":
+        $reference_cond.ref_fa
+    #else
+        NOTTHERE
+    #end if
+    #if str($include_cond.include) == "yes":
+        $include_cond.in_bed
+    #else
         NOTTHERE
     #end if
-	#if str($include_cond.include) == "yes":
-		$include_cond.in_bed
-	#else
+    #if str($exclude_cond.exclude) == "yes":
+        $exclude_cond.ex_bed
+    #else
         NOTTHERE
     #end if
-	#if str($exclude_cond.exclude) == "yes":
-		$exclude_cond.ex_bed
-	#else
+    #if $withstats:
+        $statsfile
+    #else
         NOTTHERE
     #end if
-	#for $i, $input_vcf in enumerate( $input_vcfs ):
+    #for $i, $input_vcf in enumerate( $input_vcfs ):
         "${input_vcf}"
     #end for
   </command>
 
   <inputs>
-	<param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
-	<conditional name="mix_cond">
+    <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
+
+    <conditional name="mix_cond">
         <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="mix_value" type="float" value="0.5" label="Mixture value" />
+            <param name="mix_value" type="float" value="0.5" label="Mixture value" />
         </when>
     </conditional>
-	<conditional name="cols_cond">
-        <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold.">
+
+    <conditional name="coln_cond">
+        <param name="coln" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold.">
+          <option value="yes">Specify</option>
+          <option value="no" selected="true">Do not specify</option>
+        </param>
+        <when value="yes">
+            <param name="column_ns" type="float" value="0.5" label="Column Ns value" />
+        </when>
+    </conditional>
+
+    <conditional name="colgap_cond">
+        <param name="colgap" type="select" label="Column Gaps" help="Keeps columns with fraction of gaps below specified threshold.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="column_ns" type="float" value="0.5" label="Column Ns value" />
+            <param name="column_gaps" type="float" value="0.5" label="Column gaps value" />
         </when>
     </conditional>
-	<conditional name="sample_cond">
-        <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold.">
+
+    <conditional name="samplen_cond">
+        <param name="samplen" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
+            <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
         </when>
     </conditional>
-	<conditional name="reference_cond">
+
+    <conditional name="samplegap_cond">
+        <param name="samplegap" type="select" label="Sample gaps" help="Keeps samples with fraction of gaps below specified threshold.">
+          <option value="yes">Specify</option>
+          <option value="no" selected="true">Do not specify</option>
+        </param>
+        <when value="yes">
+            <param name="sample_gaps" type="float" value="0.5" label="Sample gaps value" />
+        </when>
+    </conditional>
+
+    <conditional name="reference_cond">
         <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
+            <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
         </when>
     </conditional>
-	<conditional name="include_cond">
+
+    <conditional name="include_cond">
         <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
+            <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
         </when>
     </conditional>
-	<conditional name="exclude_cond">
+
+    <conditional name="exclude_cond">
         <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file.">
           <option value="yes">Specify</option>
           <option value="no" selected="true">Do not specify</option>
         </param>
         <when value="yes">
-			<param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
+            <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
         </when>
     </conditional>
+
   </inputs>
 
   <outputs>