diff varextract.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

--- a/varextract.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/varextract.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,11 +1,11 @@
-<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.2">
+<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.3">
   <description>from a BCF file</description>
   <macros>
     <import>toolshed_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements" />
   <version_command>python3 -m MiModD version -q</version_command>
-  <command>
+  <command> 
 	python3 -m MiModD varextract "$ifile"
 	#if $len($sitesinfo)
 	    -p
@@ -19,14 +19,14 @@
   </command>
 
   <inputs>
-      <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate the input for this tool."/>
-      <repeat name="sitesinfo" title="include information from pre-calculated vcf file" default="0">
-	      <param name="pre_vcf" type="data" format="vcf" label="independently generated vcf file" />
+      <param format="bcf" help="Use the Variant Calling tool to generate the input for this tool." label="BCF input file" name="ifile" type="data" />
+      <repeat default="0" name="sitesinfo" title="include information from pre-calculated vcf file">
+	      <param format="vcf" label="independently generated vcf file" name="pre_vcf" type="data" />
       </repeat>
-      <param name="keep_alts" type="boolean" label="keep all sites with alternate bases" truevalue="-a" falsevalue="" checked="false" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." />
+      <param checked="false" falsevalue="" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." label="keep all sites with alternate bases" name="keep_alts" truevalue="-a" type="boolean" />
   </inputs>
   <outputs>
-    <data name="output_vcf" format="vcf" label="Variants extracted with MiModd from ${on_string}"/>
+    <data format="vcf" label="Variants extracted with MiModd from ${on_string}" name="output_vcf" />
   </outputs>
 
 <help>
@@ -98,4 +98,4 @@
 
    
 </help>
-</tool>
+</tool>
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