# HG changeset patch
# User bcrain-completegenomics
# Date 1337886355 14400
# Node ID 8caa26b33983adcb0314a89feb51d75db957c0b2

Uploaded

diff -r 000000000000 -r 8caa26b33983 listvariants.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/listvariants.xml	Thu May 24 15:05:55 2012 -0400
@@ -0,0 +1,118 @@
+<tool id="cga_listvariant" name="listvariants" version="0.0.1">
+
+  <description>lists all called variants</description> <!--adds description in toolbar-->
+  
+  <command> <!--run executable-->
+    cgatools listvariants
+      --beta
+      --reference ${crr.fields.path}
+      --output $output
+      --variants 
+      #for $v in $varfiles <!--get each var file-->
+      ${v.input}
+      #end for
+      #if $include_list.listing == "yes" <!--only added when yes-->
+        --variant-listing $include_list.list
+      #end if
+      $longvar
+  </command>
+
+  <inputs>
+  	<!--form field to select crr file-->
+    <param name="crr" type="select" label="Genome build">
+      <options from_data_table="cgatools" />
+    </param>
+
+  	<!--form field to select long variants option-->
+    <param name="longvar" type="select" label="List long variants?">
+      <option value="" selected="true">no</option>
+      <option value="--list-long-variants">yes</option>
+    </param>
+
+  	<!--form fields to include existing variant list-->
+    <conditional name="include_list">
+      <param name="listing" type="select" label="Include variant listing?">
+        <option value="no" selected="true">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        <param name="list" type="data" format="tabular" label="Variant listing"/>
+      </when>
+    </conditional>
+
+  	<!--form field to select all variant files-->
+    <repeat name="varfiles" title="Var file">
+      <param name="input" type="data" format="tabular" label="Dataset">
+        <validator type="unspecified_build" />
+        <validator type="dataset_metadata_in_file" filename="cgatools.loc"
+         metadata_name="dbkey" metadata_column="0"
+         message="cgatools is not currently available for this build."/>
+      </param>
+    </repeat>
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <help>
+
+**What it does**
+
+This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
+
+cgatools: http://sourceforge.net/projects/cgatools/files/
+
+-----
+
+**cgatools Manual**::
+
+		COMMAND NAME
+			 listvariants - Lists the variants present in a variant file.
+
+		DESCRIPTION
+			 Lists all called variants present in the specified variant files, in a 
+			 format suitable for processing by the testvariants command. The output is a
+			 tab-delimited file consisting of the following columns:
+			 
+				  variantId  Sequential id assigned to each variant.
+				  chromosome The chromosome of the variant.
+				  begin      0-based reference offset of the beginning of the variant.
+				  end        0-based reference offset of the end of the variant.
+				  varType    The varType as extracted from the variant file.
+				  reference  The reference sequence.
+				  alleleSeq  The variant allele sequence as extracted from the variant 
+				             file.
+				  xRef       The xRef as extrated from the variant file.
+
+		OPTIONS
+		  -h [ --help ] 
+				  Print this help message.
+
+		  --beta 
+				  This is a beta command. To run this command, you must pass the --beta 
+				  flag.
+
+		  --reference arg
+				  The reference crr file.
+
+		  --output arg (=STDOUT)
+				  The output file (may be omitted for stdout).
+
+		  --variants arg
+				  The input variant files (may be positional args).
+
+		  --variant-listing arg
+				  The output of another listvariants run, to be merged in to produce the 
+				  output of this run.
+
+		  --list-long-variants 
+				  In addition to listing short variants, list longer variants as well 
+				  (10's of bases) by concatenating nearby calls.
+				  
+
+
+		SUPPORTED FORMAT_VERSION
+			 0.3 or later
+  </help>
+</tool>