diff snpSift_filter.xml @ 11:b884686a80dc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a

--- a/snpSift_filter.xml	Wed Apr 29 11:55:50 2015 -0400
+++ b/snpSift_filter.xml	Mon May 04 22:37:06 2015 -0400
@@ -1,12 +1,13 @@
 <tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
     <options sanitize="False" />
     <description>Filter variants using arbitrary expressions</description>
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 
+        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse
         #if $filtering.mode == 'field':
             #if $filtering.replace.pass:
                 --pass
@@ -23,6 +24,11 @@
         #end if
          > $output
     </command>
+    <configfiles>
+        <configfile name="exprFile">
+$expr#slurp
+        </configfile>
+    </configfiles>
     <inputs>
         <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." />
@@ -31,11 +37,11 @@
             <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> 
+            </param>
             <when value="entries"/>
             <when value="field">
                 <conditional name="replace">
-                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 
+                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
                            help="appends an ID tag to non-matching entry FILTER "/>
                     <when value="no"/>
                     <when value="yes">
@@ -48,16 +54,10 @@
             </when>
         </conditional>
     </inputs>
-    <configfiles>
-        <configfile name="exprFile">
-$expr#slurp
-        </configfile> 
-    </configfiles>
 
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
@@ -129,18 +129,18 @@
 
     ::
 
-    (FILTER = 'PASS') | ( na FILTER )  
+    (FILTER = 'PASS') | ( na FILTER )
 
   - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
 
     ::
-  
+
     ( EFF[*].EFFECT = 'frameshift_variant' )
 
   - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
 
     ::
-  
+
     ( EFF[*].EFFECT = 'FRAME_SHIFT' )
 
   - *I want to filter out samples with quality less than 30*:
@@ -154,23 +154,23 @@
     ::
 
     (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any homozygous variant present in more than 3 samples*:
 
     ::
 
     (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any heterozygous sample with coverage 25 or more*:
 
     ::
 
     ((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
 
     ::
-  
+
     (isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] ))