diff snpSift_annotate.xml @ 0:9e8280e19338 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_annotate.xml	Thu Jan 22 08:39:07 2015 -0500
@@ -0,0 +1,100 @@
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
+    <description>SNPs from dbSnp</description>
+    <!-- 
+        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+    -->
+    <expand macro="requirements" />
+    <macros>
+        <import>snpSift_macros.xml</import>
+    </macros>
+    <command>
+        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
+        #if $annotate.id :
+          -id
+        #elif $annotate.info_ids.__str__.strip() != '' :
+          -info "$annotate.info_ids"
+        #end if          
+        -q $dbSnp $input > $output 
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
+            help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
+        <conditional name="annotate">
+            <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
+            <when value="id"/>
+            <when value="info">
+                <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
+                    help="list is a comma separated list of fields. When blank, all INFO fields are included">    
+                    <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
+                </param>
+            </when>
+        </conditional>
+        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> 
+            <help>
+                This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
+                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 
+            </help>
+            </param>
+    </inputs>
+    <expand macro="stdio" />
+    <outputs>
+        <data format="vcf" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="vcf" value="annotate_1.vcf"/>
+            <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
+            <param name="annotate_cmd" value="False"/>
+            <param name="id" value="True"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="rs76166080" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+This is typically used to annotate IDs from dbSnp.
+
+Annotatating only the ID field from dbSnp137.vcf ::
+
+    Input VCF:
+    CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
+    22      16157571    .            T    G    0.0    FAIL    NS=53
+    22      16346045    .            T    C    0.0    FAIL    NS=244
+    22      16350245    .            C    A    0.0    FAIL    NS=192
+
+    Annotated Output VCF:
+    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
+    22      16157571    .            T    G    0.0    FAIL    NS=53
+    22      16346045    rs56234788   T    C    0.0    FAIL    NS=244
+    22      16350245    rs2905295    C    A    0.0    FAIL    NS=192
+
+
+
+Annotatating both the ID and INFO fields from dbSnp137.vcf ::
+
+    Input VCF:
+    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
+    22      16157571    .            T    G    0.0    FAIL    NS=53
+    22      16346045    .            T    C    0.0    FAIL    NS=244
+    22      16350245    .            C    A    0.0    FAIL    NS=192
+
+    Annotated Output VCF:
+    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
+    22      16157571    .            T    G    0.0    FAIL    NS=53
+    22      16346045    rs56234788   T    C    0.0    FAIL    NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
+    22      16350245    rs2905295    C    A    0.0    FAIL    NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
+
+
+@EXTERNAL_DOCUMENTATION@
+	http://snpeff.sourceforge.net/SnpSift.html#annotate
+
+@CITATION_SECTION@
+
+
+    </help>
+</tool>
+