diff table_annovar.xml @ 0:525e6995fe44 draft default tip

planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/table_annovar.xml	Mon Nov 09 11:58:50 2015 -0500
@@ -0,0 +1,126 @@
+<tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.2">
+    <description>with functional information using ANNOVAR</description>
+
+    <requirements>
+        <requirement type="package">annovar</requirement>
+        <requirement type="set_environment">SCRIPT_PATH</requirement>
+    </requirements>
+
+    <command>
+        ## Convert VCF to AV input format.
+        #if str($out_format) == "tabular":
+            convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput ;
+            #set tab_anno_input = "input.avinput"
+        #else:
+            #set tab_anno_input = $input
+        #end if
+
+        ## Variant annotation; make sure to include entry in indexes table for build database.
+
+        #set protocol = []
+        #set operation = []
+
+        ## Add gene annotations.
+        #if $gene_anns:
+            #silent protocol.append( str( $gene_anns )  )
+            #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) )
+        #end if
+
+        ## Add regions.
+        #if $regions:
+            #silent protocol.append( str( $regions ) )
+            #silent operation.append( ','.join( ['r' for t in range( str($regions).count(',') + 1 )] ) )
+        #end if
+
+        ## Add filters.
+        #if $filters:
+            #silent protocol.append( str( $filters ) )
+            #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) )
+        #end if
+
+        #set protocol = ','.join( $protocol )
+        #set operation = ','.join( $operation )
+
+        ## Annotate variants.
+        table_annovar.pl ${tab_anno_input} ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring '.' -buildver ${input.dbkey} --outfile output
+
+        ## Add option to consume/produce VCF.
+        #if str($out_format) == "vcf":
+            --vcfinput
+        #end if
+
+        ## Post-processing: process annotated table to remove "NA" strings from numerical columns if
+        ## tabular. Copy to output.
+        #if str($out_format) == "tabular":
+            ; cat output.${input.dbkey}_multianno.txt | python \${SCRIPT_PATH}/replace_NA.py > ${output}
+        #else:
+            ; cp output.${input.dbkey}_multianno.vcf ${output}
+        #end if
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
+        <validator type="unspecified_build" />
+    </param>
+
+    <param name="gene_anns" type="select" multiple="True" optional="True" label="Gene Annotations" help="" >
+        <options from_data_table="annovar_indexes">
+            <filter type="data_meta" key="dbkey" ref="input" column="1"/>
+            <filter type="static_value" name="type" value="gene_ann" column="2"/>
+        </options>
+    </param>
+
+    <param name="regions" type="select" multiple="True" optional="True" label="Annotation Regions" help="" >
+        <options from_data_table="annovar_indexes">
+            <filter type="data_meta" key="dbkey" ref="input" column="1"/>
+            <filter type="static_value" name="type" value="region" column="2"/>
+        </options>
+    </param>
+
+    <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" >
+        <options from_data_table="annovar_indexes">
+            <filter type="data_meta" key="dbkey" ref="input" column="1"/>
+            <filter type="static_value" name="type" value="filter" column="2"/>
+        </options>
+    </param>
+
+    <param name="out_format" type="select" label="Output data type">
+        <option value="vcf">VCF</option>
+        <option value="tabular">Tabular</option>
+    </param>
+
+    </inputs>
+
+    <stdio>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+
+    <outputs>
+        <data name="output" format="tabular">
+            <change_format>
+                <when input="out_format" value="vcf" format="vcf"/>
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+**What it does**
+
+This tool will annotate variants using specified gene annotations, regions, and filtering databases. Input is a VCF dataset, and output is a table of annotations for each variant in the
+VCF dataset or a VCF dataset with the annotations in INFO fields.
+
+**ANNOVAR Website and Documentation**
+
+Website: http://www.openbioinformatics.org/annovar/
+
+Paper: http://nar.oxfordjournals.org/content/38/16/e164
+
+**Important Usage Note**
+
+ANNOVAR is open-source and free for non-profit use. If you use it for commercial purposes, please contact BIOBASE ([e-mail]) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license
+
+    </help>
+</tool>