diff VCFToolFilter/vcfToolsFilter.xml @ 3:612066e3f57d draft

Uploaded

--- a/VCFToolFilter/vcfToolsFilter.xml	Fri Jul 10 04:16:17 2015 -0400
+++ b/VCFToolFilter/vcfToolsFilter.xml	Mon Nov 09 05:18:45 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.1">
+<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> </description>
@@ -9,16 +9,16 @@
 	<requirement type="package" version="0.1.12b">vcftools</requirement>
     </requirements>
     
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
+
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>    
+
     <!-- [REQUIRED] The command to execute -->
     <command interpreter="perl">
-	vcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
+	vcfToolsFilter.sh $filein $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
 	#if str( $samples ) == "":
 	'None'
 	#else
@@ -55,7 +55,7 @@
 	<param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." />
 	<param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
 	<param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" />
-	<param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" />
+	<param name="nb_alleles_max" type="integer" value="4" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" />
         <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
             <option value="ALL" selected="true">All</option>
             <option value="SNP">SNP</option>
@@ -73,17 +73,12 @@
 			<when input="export" value="plink" format="txt" />
 		</change_format>	
 	</data>
-	<data name="fileout_map" format="txt" label="${fileout_label}.map">
+	<data name="fileout_map" format="tabular" label="${fileout_label}.map">
 		<filter>(export == 'plink')</filter>
 	</data>
 	<data name="filelog" format="txt" label="${fileout_label}.log" />
     </outputs>
     
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
     
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
@@ -101,7 +96,19 @@
          <param name="bound_start" value="1" />
          <param name="bound_end" value="100000000" />
          <output name="fileout" file="result.vcf" />
-         <output name="filelog" file="result.log" />
+        </test>
+	<test>
+         <param name="filein" value="sample.vcf" />
+         <param name="export" value="plink" />
+         <param name="type_p" value="SNP" />
+         <output name="fileout" file="result.ped" />
+	  <output name="fileout_map" file="result.map" />
+        </test>
+	<test>
+         <param name="filein" value="sample.vcf" />
+         <param name="export" value="freq" />
+         <param name="type_p" value="ALL" />
+         <output name="fileout" file="result.frq" />
         </test>
     </tests>