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changeset 16:4f338a8e39b3 draft

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Deleted selected files
author bcrain-completegenomics
date Tue, 12 Jun 2012 13:28:37 -0400
parents 9ab17046b3d8
children b5d625104ba1
files cgatools/._tool_config.xml.sample.xml cgatools/._tool_data_table_conf.xml.sample cgatools/._tool_data_table_conf.xml.sample.xml cgatools/tool_config.xml.sample.xml cgatools/tool_data_table_conf.xml.sample cgatools/tool_data_table_conf.xml.sample.xml cgatools/tools/cgatools/._calldiff.xml cgatools/tools/cgatools/._join.xml cgatools/tools/cgatools/._junctiondiff.xml cgatools/tools/cgatools/._listtestvariants.xml cgatools/tools/cgatools/._listvariants.xml cgatools/tools/cgatools/._snpdiff.xml cgatools/tools/cgatools/._testing.pl cgatools/tools/cgatools/._testvariants.xml cgatools/tools/cgatools/._varfilter.xml cgatools/tools/cgatools/._varfilter_wrapper.pl cgatools/tools/cgatools/calldiff.xml cgatools/tools/cgatools/snpdiff.xml cgatools/tools/cgatools/testing.pl listtestvariants.xml
diffstat 20 files changed, 75 insertions(+), 286 deletions(-) [+]
line wrap: on
line diff
Binary file cgatools/._tool_config.xml.sample.xml has changed
Binary file cgatools/._tool_data_table_conf.xml.sample has changed
Binary file cgatools/._tool_data_table_conf.xml.sample.xml has changed
--- a/cgatools/tool_config.xml.sample.xml	Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-    <!-- 
-      Add the following section to tool_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
-    -->
-  <section name="Complete Genomics" id="cgi">
-    <label text="cgatools" id="cgi_cgatools" />
-    <tool file="cgatools/listvariants.xml" />
-    <tool file="cgatools/testvariants.xml" />
-    <tool file="cgatools/listtestvariants.xml" />
-    <tool file="cgatools/join.xml" />
-    <tool file="cgatools/calldiff.xml" />
-    <tool file="cgatools/snpdiff.xml" />
-    <tool file="cgatools/junctiondiff.xml" />
-    <tool file="cgatools/varfilter.xml" />
-    <label text="Perl scripts" id="cgi_perl" />
-    <tool file="cgi_scripts/List_Unique_Variants.xml" />
-    <tool file="cgi_scripts/Calculate_TestVariants_Variant_Frequencies.xml" />
-  </section>
-</toolbox>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools/tool_data_table_conf.xml.sample	Tue Jun 12 13:28:37 2012 -0400
@@ -0,0 +1,9 @@
+    <!-- 
+         Add the following section to tool_data_table_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
+    -->
+    <!-- Start Location of cgatools crr files -->
+    <table name="cg_crr_files" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/cg_crr_files.loc" />
+    </table>
+    <!-- End Location of cgatools crr files -->
--- a/cgatools/tool_data_table_conf.xml.sample.xml	Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<tables>
-    <!-- 
-         Add the following section to tool_data_table_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
-    -->
-    <!-- Start Location of cgatools crr files -->
-    <table name="cg_crr_files" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/cg_crr_files.loc" />
-    </table>
-    <!-- End Location of cgatools crr files -->
-</tables>
-
Binary file cgatools/tools/cgatools/._calldiff.xml has changed
Binary file cgatools/tools/cgatools/._join.xml has changed
Binary file cgatools/tools/cgatools/._junctiondiff.xml has changed
Binary file cgatools/tools/cgatools/._listtestvariants.xml has changed
Binary file cgatools/tools/cgatools/._listvariants.xml has changed
Binary file cgatools/tools/cgatools/._snpdiff.xml has changed
Binary file cgatools/tools/cgatools/._testing.pl has changed
Binary file cgatools/tools/cgatools/._testvariants.xml has changed
Binary file cgatools/tools/cgatools/._varfilter.xml has changed
Binary file cgatools/tools/cgatools/._varfilter_wrapper.pl has changed
--- a/cgatools/tools/cgatools/calldiff.xml	Tue Jun 12 13:27:50 2012 -0400
+++ b/cgatools/tools/cgatools/calldiff.xml	Tue Jun 12 13:28:37 2012 -0400
@@ -123,9 +123,9 @@
 				<option value="SomaticOutput">yes</option>
 			</param>
 			<when value="SomaticOutput">
-				<param name="genomeA" type="text" size="300" label="Directory for genome A (path/dir)" help="The 'A' genome directory, for example /data/GS00118-DNA_A01; this directory is expected to contain ASM/REF and ASM/EVIDENCE subdirectories."/>
-				<param name="genomeB" type="text" size="300" label="Directory for genome B (path/dir)" help="The 'B' genome directory"/>
-				<param name="calibration" type="text" size="300" label="Directory calibration data (path/dir)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v1.tgz"/>
+				<param name="genomeA" type="text" size="300" label="Directory for genome A (/path/dir)" help="The 'A' genome directory, for example /data/GS00118-DNA_A01; this directory is expected to contain ASM/REF and ASM/EVIDENCE subdirectories."/>
+				<param name="genomeB" type="text" size="300" label="Directory for genome B (/path/dir)" help="The 'B' genome directory"/>
+				<param name="calibration" type="text" size="300" label="Directory calibration data (/path/dir)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v1.tgz"/>
 			</when>
 		</conditional>
 		
--- a/cgatools/tools/cgatools/snpdiff.xml	Tue Jun 12 13:27:50 2012 -0400
+++ b/cgatools/tools/cgatools/snpdiff.xml	Tue Jun 12 13:28:37 2012 -0400
@@ -7,14 +7,75 @@
   </requirements>
 
   <command> <!--run executable-->
-  	cgatools snpdiff --beta -h
+  	cgatools snpdiff 
+  	--reference $crr.fields.path 
+  	--variants $varfile
+  	--genotypes $genotype
+  	--output-prefix cg_
+  	--reports `echo ${report1} ${report2} ${report3} | sed 's/  */,/g'` 
   </command>
 
   <outputs>
-  	<data format="tabular" name="output" />
+  	<data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="${tool.name} on ${on_string}: Output">
+  	<filter>(report1 == 'Output')</filter>
+  	</data>
+  	<data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="${tool.name} on ${on_string}: Verbose">
+  	<filter>(report2 == 'Verbose')</filter>
+  	</data>
+  	<data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="${tool.name} on ${on_string}: Stats">
+  	<filter>(report3 == 'Stats')</filter>
+  	</data>
   </outputs>
   
   <inputs>
+		<!--form field to select crr file-->
+		<param name="crr" type="select" label="Genome build">
+			<options from_data_table="cg_crr_files" />
+		</param>
+	
+		<!--conditional to select variant file input-->
+  	<conditional name="data_sources">
+      <param name="data_source" type="select" label="Where is the input varfile?">
+        <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-->
+				<param name="varfile" type="data" format="cg_var" label="Var file">
+					<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>
+      <when value="out">
+				<!--form field to select crr file-->
+				<param name="varfile" type="text" label="Variant file (/path/file_name)" size="40" help="Variant file can be compressed (gz, bz2)."/>
+			</when>
+		</conditional>
+
+		<!--conditional to select genotypes file input-->
+		<param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at 
+    least the following columns (additional columns may be given): Chromosome (Required), Offset0Based (Required), GenotypesStrand (Optional), Genotypes (Optional)">
+			<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>
+
+		<param name="report1" type="select" label="Report Output">
+			<option value="">no</option>
+			<option value="Output">yes</option>
+		</param>
+		<param name="report2" type="select" label="Report Verbose">
+			<option value="">no</option>
+			<option value="Verbose">yes</option>
+		</param>
+		<param name="report3" type="select" label="Report Stats">
+			<option value="">no</option>
+			<option value="Stats">yes</option>
+		</param>
+
   </inputs>
 
   <help>
--- a/cgatools/tools/cgatools/testing.pl	Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/usr/bin/perl
-
-print "$0 @ARGV\n";
-open OUT, ">@ARGV[0]";
-print "test1 ok\ttest1 ok\ntest1 ok\ttest1 ok\n";
-print OUT "test ok\ttest ok\ntest ok\ttest ok\n";
-close OUT;
-open OUT, ">somefile";
-print OUT "test2 ok\ttest2 ok\ntest2 ok\ttest2 ok\n";
-close OUT;
\ No newline at end of file
--- a/listtestvariants.xml	Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-<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>