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changeset 14:4851ac12f704 draft

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Uploaded
author bcrain-completegenomics
date Tue, 12 Jun 2012 13:26:56 -0400
parents 63541ee5f319
children 9ab17046b3d8
files listtestvariants.xml
diffstat 1 files changed, 239 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/listtestvariants.xml	Tue Jun 12 13:26:56 2012 -0400
@@ -0,0 +1,239 @@
+<tool id="cga_listtestvariants" name="listvariants(beta)-testvariants(beta)" version="1.0.1">
+<!--
+This tool creates a GUI for cgatools listvariants and testvariants from Complete Genomics, Inc.
+to be run consecutively with the same input files.
+written 5-29-2012 by bcrain@completegenomics.com
+-->
+
+  <description></description> <!--adds description in toolbar-->
+
+  <requirements>
+  	<requirement type="binary">cgatools</requirement>
+  </requirements>
+
+  <command> <!--run executable-->
+		cgatools listvariants
+		--beta
+		--reference ${crr.fields.path}
+		--output $output1
+		#if $include_list.listing == "yes" <!--only added when yes-->
+			--variant-listing $include_list.list
+		#end if
+		$longvar
+		--variants 
+		#if $file_types.data_sources.data_source == "in" 
+			#for $v in $file_types.data_sources.varfiles <!--get each var file-->
+				${v.input}
+			#end for
+		#else
+			`cat $file_types.data_sources.varlist`
+		#end if
+		;
+    
+		cgatools testvariants
+		--beta
+		--reference ${crr.fields.path}
+		--output $output2
+		--input $output1
+		--variants 
+		#if $file_types.data_sources.data_source == "in" 
+			#for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
+				${v.input}
+			#end for
+		#else
+			`cat $file_types.data_sources.varlist`
+		#end if
+  </command>
+
+  <outputs>
+    <data format="tabular" name="output1" label="listvariants output"/>
+    <data format="tabular" name="output2" label="testvariants output"/>
+  </outputs>
+  
+  <inputs>
+  	<!--form field to select crr file-->
+    <param name="crr" type="select" label="Genome build">
+      <options from_data_table="cg_crr_files" />
+    </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">
+        <validator type="unspecified_build" />
+						<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+						 metadata_name="dbkey" metadata_column="1"
+						 message="cgatools is not currently available for this build."/>
+        </param>
+      </when>
+    </conditional>
+
+		<!--conditional to select input file type-->
+  	<conditional name="file_types">
+      <param name="file_type" type="select" label="Select the input file type">
+        <option value="var" selected="true">var files</option>
+        <option value="mastervar">mastervar files</option>
+      </param>
+      
+      <when value="var">			
+				<!--conditional to select variant file input-->
+				<conditional name="data_sources">
+					<param name="data_source" type="select" label="Where are the input var files?">
+						<option value="in" selected="true">imported into Galaxy</option>
+						<option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
+					</param>
+					<when value="in">
+						<!--form field to select variant files-->
+						<repeat name="varfiles" title="Variant files">
+							<param name="input" type="data" format="cg_var" label="Dataset">
+								<validator type="unspecified_build" />
+								<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+								 metadata_name="dbkey" metadata_column="1"
+								 message="cgatools is not currently available for this build."/>
+							</param>
+						</repeat>
+					</when>
+					<when value="out">
+						<!--form field to select crr file-->
+						<param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, bz2)."/>
+					</when>
+				</conditional>
+			</when>
+			
+	    <when value="mastervar">			
+				<!--conditional to select variant file input-->
+				<conditional name="data_sources">
+					<param name="data_source" type="select" label="Where are the input mastervar files?">
+						<option value="in" selected="true">imported into Galaxy</option>
+						<option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
+					</param>
+					<when value="in">
+						<!--form field to select variant files-->
+						<repeat name="varfiles" title="Variant files">
+							<param name="input" type="data" format="cg_mastervar" label="Dataset">
+								<validator type="unspecified_build" />
+								<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
+								 metadata_name="dbkey" metadata_column="1"
+								 message="cgatools is not currently available for this build."/>
+							</param>
+						</repeat>
+					</when>
+					<when value="out">
+						<!--form field to select crr file-->
+						<param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="file with list of mastervar files (/path/varfile), mastervar files can be compressed (gz, bz2)."/>
+					</when>
+				</conditional>
+			</when>
+		</conditional>
+  </inputs>
+
+  <help>
+  
+**What it does**
+
+This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
+
+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
+		
+		
+		
+		COMMAND NAME
+		  testvariants - Tests variant files for presence of variants.
+		
+		DESCRIPTION
+		  Tests variant files for presence of variants. The output is a tab-delimited
+		  file consisting of the columns of the input variants file, plus a column 
+		  for each assembly results file that contains a character code for each 
+		  allele. The character codes have meaning as follows:
+			
+		    0 This allele of this genome is consistent with the reference at this 
+		      locus but inconsistent with the variant.
+		    1 This allele of this genome has the input variant at this locus.
+		    N This allele of this genome has no-calls but is consistent with the 
+		      input variant.
+		
+		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.
+		
+		  --input arg (=STDIN)
+		      The input variants to test for.
+		
+		  --output arg (=STDOUT)
+		      The output file (may be omitted for stdout).
+		
+		  --variants arg
+		      The input variant files (may be passed in as arguments at the end of 
+		      the command).
+		
+		SUPPORTED FORMAT_VERSION
+		  0.3 or later			
+  </help>
+</tool>