diff snpSift_caseControl.xml @ 2:bf8c1526871b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

--- a/snpSift_caseControl.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_caseControl.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,6 +1,6 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1">
     <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)
     -->
     <macros>
@@ -10,16 +10,17 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
-    #if str($name).strip() != '':
-      -name "$name"
-    #end if
-    #if $ctrl.ctrl_src == 'caseString':
-      '$ctrl.caseControlStr' 
-    #else
-      -tfam "$ctrl.tfam"
-    #end if
-    "$input" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q
+        #if str($name).strip() != '':
+            -name "$name"
+        #end if
+        #if $ctrl.ctrl_src == 'caseString':
+            '$ctrl.caseControlStr'
+        #else
+            -tfam "$ctrl.tfam"
+        #end if
+        "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -41,8 +42,8 @@
             <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
         </when>
         </conditional>
-        <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
-            <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
+        <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags">
+            <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
         </param>
     </inputs>
     <outputs>
@@ -90,13 +91,13 @@
 
 **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.*
 
@@ -110,7 +111,7 @@
 
   - Hom/Het case = "hom"
 
-  - Hom/Het control = "any"  
+  - Hom/Het control = "any"
 
   - Case / Control column designation = ""++++------"