diff vcffilter.xml @ 0:34c3b846e0b6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcffilter.xml	Thu Mar 19 14:27:51 2015 -0400
@@ -0,0 +1,78 @@
+<tool id="vcffilter2" name="VCFfilter:" version="0.0.3">
+  <description>filter VCF data in a variety of attributes</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="0.2.6">tabix</requirement>
+  </expand>
+  <expand macro="stdio" />
+  <command>
+  <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
+    ln -s "${input1}" input1.vcf &amp;&amp;
+    bgzip input1.vcf &amp;&amp;
+    tabix -p vcf input1.vcf.gz &amp;&amp;
+    vcffilter ${filterList} input1.vcf.gz  > "${out_file1}"
+  </command>
+  
+  <inputs>
+    <param name="filterList" size="40" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
+      <sanitizer>
+        <valid initial="string.printable">
+	  <remove value="&apos;"/>
+        </valid>
+        <mapping initial="none">
+          <add source="&apos;" target="__sq__"/>
+        </mapping>
+      </sanitizer>
+    </param>
+    <param format="vcf" name="input1" type="data" label="VCF dataset to filter">
+    </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+ <tests>
+    <test>
+      <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
+      <param name="input1" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcffilter-test1.vcf"/>
+    </test>
+</tests> 
+ <help>
+
+You can specify the following options within the **Specify filtering expression** box in any combination::
+
+    -f, --info-filter     specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
+    -g, --genotype-filter specifies a filter to apply to the genotype fields of records
+    -s, --filter-sites    filter entire records, not just alleles
+    -t, --tag-pass        tag vcf records as positively filtered with this tag, print all records
+    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
+    -A, --append-filter   append the existing filter tag, don't just replace it
+    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
+    -v, --invert          inverts the filter, e.g. grep -v
+    -o, --or              use logical OR instead of AND to combine filters
+    -r, --region          specify a region on which to target the filtering (must be used in conjunction with -f or -g)
+
+Filters are specified in the form {ID} {operator} {value}::
+
+ -f "DP > 10"          # for info fields
+ -g "GT = 1|1"         # for genotype fields
+ -f "CpG"              # for 'flag' fields
+
+Any number of filters may be specified.  They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.  
+
+Operators can be any of: =, !, &lt;, &gt;, pipe, &amp;
+
+
+To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
+
+ -r chr20:14000-15000  # only output calls between positions 14,000 and 15,000 on chromosome 20
+ -r chrX               # only output call on chromosome X
+
+-----
+
+Vcffilter @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>