diff snpSift_filter.xml @ 7:0ad9733e22a4

Uploaded

--- a/snpSift_filter.xml	Thu Nov 28 08:16:11 2013 -0600
+++ b/snpSift_filter.xml	Fri Nov 29 09:27:22 2013 -0500
@@ -1,9 +1,10 @@
 <tool id="snpSift_filter" name="SnpSift Filter" version="3.4">
     <options sanitize="False" />
     <description>Filter variants using arbitrary expressions</description>
-    <requirements>
-        <requirement type="package" version="3.4">snpEff</requirement>
-    </requirements>
+    <expand macro="requirements" />
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
     <command>
         java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 
         #if $filtering.mode == 'field':
@@ -23,11 +24,11 @@
          > $output
     </command>
     <inputs>
-        <param format="vcf" name="input" type="data" label="VCF input"/>
-        <param name="expr" type="text" label="Expression" size="160"/>
-        <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/>
+        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." />
+        <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
         <conditional name="filtering">
-            <param name="mode" type="select" labael="Filter mode">
+            <param name="mode" type="select" label="Filter mode">
                 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
                 <option value="field">Change the FILTER field, but retain all entries</option>
             </param> 
@@ -56,13 +57,8 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <stdio>
-      <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-      <exit_code range="1:"  level="fatal"   description="Error" />
-    </stdio>
-
+    <expand macro="stdio" />
     <tests>
-
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
         <param name="expr" value="QUAL >= 50"/>
@@ -114,9 +110,7 @@
             </assert_contents>
         </output>
         </test>
-
     </tests>
-
     <help>
 
 **SnpSift filter**
@@ -146,14 +140,9 @@
     * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**
 
 
-For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
+@EXTERNAL_DOCUMENTATION@
 
-SnpEff citation:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
-
+@CITATION_SECTION@
 
     </help>
 </tool>