# HG changeset patch
# User anton
# Date 1410806890 14400
# Node ID 260173250dd217967d27f0c30cf19684a8eeacad
# Parent  971da09d28aa6b45e576e7deced359a2075caafd
Uploaded

diff -r 971da09d28aa -r 260173250dd2 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 25 16:34:01 2014 -0400
+++ b/tool_dependencies.xml	Mon Sep 15 14:48:10 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="vcflib" version="86723982aa">
-      <repository changeset_revision="a6826babf644" name="vcflib_86723982aa" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="bffe0495cd92" name="package_vcflib_8a5602bf07" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 971da09d28aa -r 260173250dd2 vcfallelicprimitives.xml
--- a/vcfallelicprimitives.xml	Wed Jun 25 16:34:01 2014 -0400
+++ b/vcfallelicprimitives.xml	Mon Sep 15 14:48:10 2014 -0400
@@ -1,41 +1,61 @@
+<?xml version="1.0" encoding="utf-8"?>
 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.2">
-<requirements>
-    <requirement type="package" version="86723982aa">vcflib</requirement>
-</requirements>
-  <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
-  <command>cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" > "${out_file1}"</command>
-  <inputs>
-    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
-    <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
-    <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="--tag-parsed option"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="m_option" value="true"/>
-      <param name="t_option" value="Split primitives"/>
-      <param name="input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/>
-    </test>
+    <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
+    <requirements>
+        <requirement type="package" version="8a5602bf07">vcflib</requirement>
+    </requirements>
+    <command>
+        cat "${input}" | vcfallelicprimitives 
+            ${m_option} 
+            -t "${t_option}"
+	    -L "${max_length}" 
+            $keep_info 
+            $keep_geno > "${out_file1}"
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
+        <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
+        <param name="t_option" size="20" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/>
+	<param name="max_length" type="integer" size="4" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/>
+        <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False" 
+            label="Maintain site and allele-level annotations when decomposing" 
+            help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition.  For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/>
+        <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False" 
+            label="Maintain genotype-level annotations when decomposing" 
+            help="Similar caution should be used for this as for --keep-info. (--keep-geno)"/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/>
+        </test>
     </tests>
-  <help>
+    <help>
 
-If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields.  "Pure" MNPs are split into multiple SNPs unless the -m flag is provided.  Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
+If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields.  
+"Pure" MNPs are split into multiple SNPs unless the -m flag is provided. 
+Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
 
 The options are::
-                                                                                                                           
-    --use-mnps (-m)
-    Retain MNPs as separate events                                                                          
-    
-    --tag-parsed (-t) FLAG
-    Tag records which are split apart of a complex allele                                                                                                                                                             
-    with this flag                                                 
+
+    -m, --use-mnps          Retain MNPs as separate events (default: false).
+    -t, --tag-parsed FLAG   Tag records which are split apart of a complex allele with this flag.
+    -L, --max-length LEN    Do not manipulate records in which either the ALT or
+                            REF is longer than LEN (default: 200).
+    -k, --keep-info         Maintain site and allele-level annotations when decomposing.
+                            Note that in many cases, such as multisample VCFs, these won't
+                            be valid post-decomposition.  For biallelic loci in single-sample
+                            VCFs, they should be usable with caution.
+    -g, --keep-geno         Maintain genotype-level annotations when decomposing.  Similar
+                            caution should be used for this as for --keep-info.
 
 ----
 
-Vcfallelicprimitives is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+Vcfallelicprimitives is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
 
-</help>
+    </help>
 </tool>
+