Mercurial > repos > elixir-it > covacs_variant_recalibrator

--- a/covacs_VariantRecalibrator.xml	Fri Nov 09 06:52:10 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
- <tool id="covacs_VarianRecalibrator" name="covacs_VariantRecalibrator" version="3.8">
-  <description>GATK VariantRecalibrator wrapper Version = 3.8</description>
-  <macros>
-	<import>bed_macros.xml</import>
-	<import>vcf_macros.xml</import>
-  </macros>
-  <requirements>
-  	<requirement type="package" version="3.8" >gatk</requirement>
-  </requirements>
-  <command>
-    <![CDATA[
-	### call the .sh to untar the package
-        sh $__tool_directory__/mv_untar_gatk.sh &&
-
-	##sym link to run GATK
-	 #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
-         ln -s $bed_source.bed_history region.bed &&
-	#end if
-
-	ln -s $input1 input1.vcf &&
-
-	##GATK tool call
-	java -jar  \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -T VariantRecalibrator
-
-
-
-	#if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
-        -L  region.bed
-        #end if
-        #if $bed_source.bed_source_selector == "cached"
-        -L $bed_source.bed_cached.fields.path
-        #end if
-
-
-
-	-ip $ip
-	##call chose genome from covacs_gatk_indexes.loc
-      		-R $ref_file.fields.path
-
-	##vcf input parameter
-
-	-input input1.vcf
-
-	## for that permit to insert different resources
-
-	#for $r in $resource#
-
-		#if $r.vcf_source.vcf_source_selector == "history" and $r.vcf_source.vcf_history
-
-        	--resource:${r.nameresource},known=${r.known.value},training=${r.training.value},truth=${r.truth.value},prior=${r.prior.value} ${r.vcf_source.vcf_history}
-		#end if
-
-       	 	#if $r.vcf_source.vcf_source_selector == "cached"
-
-        	--resource:${r.nameresource},known=${r.known.value},training=${r.training.value},truth=${r.truth.value},prior=${r.prior.value} ${r.vcf_source.vcf_cached.fields.path}
-		#end if
-
-	#end for
-
-	-mode $mode_type.mode
-	##chose between INDEL and SNP call
-
-	#if $mode_type.mode == "INDEL"
-		--minNumBadVariants $mode_type.minNumBadVariants
-		--maxGaussians $mode_type.maxGaussian
-		-mNG $mode_type.mNG
-	#end if
-
-	## for that permit to insert different resources
-
-	#for $a in $an#
-
-		-an ${a.an_name.value}
-
-	#end for
-
-	## for that permit to insert different resources
-
-	#for $t in $tranches_name#
-
-		-tranche ${t.tranches.value}
-	#end for
-
-	##outputs
-
-	-recalFile $recal
-	-tranchesFile $tranches
-
-	2> $log
-	]]>
-  </command>
-  <inputs>
-    <param name="ref_file" type="select" label="Using indexed reference genome" help="Select indexed genome from the list">
-       <options from_data_table="covacs_gatk_indexes">
-         <filter type="sort_by" column="2" />
-         <validator type="no_options" message="No indexes are available" />
-       </options>
-       <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-    </param>
-    <param format="vcf" name="input1" label="VCF of raw input variants to be recalibrated" type="data" optional="true" />
-    <expand macro="bed_loc"/>
-    <param name="ip" type="integer" value="100" help="Amount of padding (in bp) to add to each interval"/>
-    <repeat name="resource" title="-resource" help="A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run)">
-      <expand macro="vcf_loc"/>
-      <param name="nameresource" label="name of the resource" type="select" >
-	<option value="hapmap">hapmap</option>
-	<option value="omni">omni</option>
-	<option value="1000G">1000G</option>
-	<option value="mills">mills</option>
-	<option value="dbsnp">dbsnp</option>
-      </param>
-      <param name="known" type="select" display="radio" help="Known - The program only uses known sites for reporting purposes (to indicate whether variants are already known or novel)" >
-	<option value="true">true</option>
-	<option value="false">false</option>
-      </param>
-      <param name="training" type="select" display="radio" help="Training - The program builds the Gaussian mixture model using input variants that overlap with these training sites.">
-	<option value="true">true</option>
-	<option value="false">false</option>
-      </param>
-      <param name="truth" type="select" display="radio" help="Truth - The program uses these truth sites to determine where to set the cutoff in VQSLOD sensitivity">
-	<option value="true">true</option>
-	<option value="false">false</option>
-      </param>
-      <param name="prior" value="10.0" min="0" max="100.0" type="float"/>
-    </repeat>
-   <repeat name="an" title="-an" help="Annotation which should used for calculations">
-      <param name="an_name" label="annotation name" type="select"  help="The name of the annotation which should used for calculations">
-	<option value="DP">DP</option>
-	<option value="QD">QD</option>
-	<option value="MQRankSum">MQRankSum</option>
-	<option value="ReadPosRankSum">ReadPosRankSum</option>
-	<option value="FS">FS</option>
-       </param>
-    </repeat>
-    <repeat name="tranches_name" title="tranches" help="The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent)">
-      <param name="tranches" value="98.0" min="0" max="100.0" type="float"/>
-    </repeat>
-    <conditional name="mode_type">
-    	<param name="mode" type="select" display="radio" help=" Recalibration mode to employ (SNP|INDEL)">
-		<option value="SNP">snp</option>
-		<option value="INDEL">INDEL</option>
-    	</param>
-    	<when value="INDEL">
-		<param name="maxGaussian" type="integer" value="4"/>
-		<param name="minNumBadVariants" type="integer" value="5000"/>
-		<param name="mNG" type="integer" value="2"/>
-    	</when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format="txt" name="recal" from_work_dir="recal" label="${tool.name} on ${on_string}:recal"/>
-    <data format="txt" name="tranches" from_work_dir="tranches" label="${tool.name} on ${on_string}:tranches"/>
-    <data format="txt" name="log" label="log"/>
-  </outputs>
-  <help>
-.. class:: warningmark
-
-**IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK version 3.8 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file
-
-		**more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php
-
------
-
-**Implemented options** VariantRecalibrator:
-
-**-L**                   : One or more genomic intervals over which to operate(file.bed)
-
-**-ip**                  Amount of padding (in bp) to add to each interval
-
-**--resource:NAME,known=true/false,training=true/false,truth=true/false,prior=float $file**   :A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run)
-
-**-mode**   : Recalibration mode to employ (SNP|INDEL)
-
-**-an** : annotations which should used for calculations
-
-**-tranche**     The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent)
-
-**in case of indels mode**
-
-**--minNumBadVariants**   : Minimum number of bad variants
-
-**--maxGaussians**        : Max number of Gaussians for the positive model
-
-**-mNG**                  : Max number of Gaussians for the negative model
-
-**OUTPUTS**
-
--recalFile
-
--tranchesFile
-
------
-
-.. class:: infomark
-
-**Recommended CoVaCS command**
-
-**-ip** 100
-
-**-R** genome.fa
-
-**-input** VCF
-
-**-resource**:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap.vcf
-
-**-resource**:omni,known=false,training=true,truth=true,prior=12.0 omni.vcf
-
-**-resource**:1000G,known=false,training=false,truth=false,prior=8.0 1000G.vcf
-
-**-resource**:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp.vcf
-
-**-mode** SNP
-
-**-an** DP **-an** QD **-an** MQ **-an** MQRankSum **-an** ReadPosRankSum **-an** FS
-
-**-tranche** 100.0 **-tranche** 99.5 **-tranche** 99.0 **-tranche** 98.5 **-tranche** 90.0
-
-  </help>
-  <citations>
-        <citation type="doi">10.1186/s12864-018-4508-1</citation>
-  </citations>
-</tool>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Nov 09 06:53:04 2018 -0500
@@ -0,0 +1,17 @@
+<tables>
+ <!-- Location of bed-file for covacs -->
+    <table name="covacs_bed" comment_char="#">
+        <columns> value, dbkey, name, path</columns>
+        <file path="tool-data/covacs_bed.loc" />
+    </table>
+<!-- Location of index file  for covacs gatk wrapper -->
+    <table name="covacs_gatk_indexes" comment_char="#">
+        <columns> value, dbkey, name, path</columns>
+        <file path="tool-data/covacs_gatk_indexes.loc" />
+    </table>
+<!-- Location of vcf-file for covacs VariantRecalibrator -->
+    <table name="covacs_vcf" comment_char="#">
+        <columns> value, name, path</columns>
+        <file path="tool-data/covacs_vcf.loc" />
+    </table>
+</tables>