changeset 3:a2b8590be75e draft

Deleted selected files

--- a/listvariants.xml	Thu May 24 15:16:40 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-<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>