Mercurial > repos > iuc > snpsift

diff snpSift_caseControl.xml @ 11:b884686a80dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:06 -0400
parents f0faaa4d6ee5
children 6bf58286d795
line wrap: on
line diff
--- a/snpSift_caseControl.xml	Wed Apr 29 11:55:50 2015 -0400
+++ b/snpSift_caseControl.xml	Mon May 04 22:37:06 2015 -0400
@@ -1,19 +1,20 @@
 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0">
     <description>Count samples are in 'case' and 'control' groups.</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>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
-    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
+    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
     #if $name.__str__.strip() != '':
       -name $name
     #end if
     #if $ctrl.ctrl_src == 'caseString':
-      '$ctrl.caseControlStr' 
+      '$ctrl.caseControlStr'
     #else
       -tfam "$ctrl.tfam"
     #end if
@@ -45,7 +46,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="test.private.01.vcf"/>
@@ -88,13 +88,13 @@
 
 **SnpSift CaseControl**
 
-Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 
+Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
 
-Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 
+Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
 
 This command adds two annotations to the VCF file:
 
- - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 
+ - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
 
   "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
 
@@ -108,7 +108,7 @@
 
   - Hom/Het case = "hom"
 
-  - Hom/Het control = "any"  
+  - Hom/Het control = "any"
 
   - Case / Control column designation = ""++++------"