diff VCFToolFilter/vcfToolsFilter.xml @ 6:1420a55ca72b draft

planemo upload

--- a/VCFToolFilter/vcfToolsFilter.xml	Mon Feb 15 11:29:42 2016 -0500
+++ b/VCFToolFilter/vcfToolsFilter.xml	Mon Mar 21 10:22:36 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2">
+<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.2.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> </description>
@@ -18,7 +18,7 @@
 
     <!-- [REQUIRED] The command to execute -->
     <command interpreter="perl">
-	vcfToolsFilter.sh $filein $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
+	vcfToolsFilter.sh $input $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
 	#if str( $samples ) == "":
 	'None'
 	#else
@@ -35,17 +35,13 @@
 	''
 	#end if
     </command>
-     
+    <code file="find_indiv.py"/>
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
-	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
+	<param name="input" type="data" format="vcf" optional="false" label="VCF input" />
 	<param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/>
-	<param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list">
-		<validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator>
-	</param>
-	<param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list">
-	        <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator>
-        </param>
+	<param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(input)" help="Samples to be analyzed." />
+        <param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />
 	<param name="export" type="select" label="Output format" >
 	    <option value="VCF" selected="true">VCF</option>
 	    <option value="freq">freq</option>
@@ -84,7 +80,7 @@
     <tests>
         <!-- [HELP] Test files have to be in the ~/test-data directory -->
         <test>
-         <param name="filein" value="sample.vcf" />
+         <param name="input" value="sample.vcf" />
          <param name="chromosomes" value="chr1" />
          <param name="export" value="VCF" />
          <param name="frequency" value="0.001" />
@@ -98,14 +94,14 @@
          <output name="fileout" file="filter-result.vcf" />
         </test>
 	<test>
-         <param name="filein" value="sample.vcf" />
+         <param name="input" value="sample.vcf" />
          <param name="export" value="plink" />
          <param name="type_p" value="SNP" />
          <output name="fileout" file="filter-result.ped" />
 	  <output name="fileout_map" file="filter-result.map" />
         </test>
 	<test>
-         <param name="filein" value="sample.vcf" />
+         <param name="input" value="sample.vcf" />
          <param name="export" value="freq" />
          <param name="type_p" value="ALL" />
          <output name="fileout" file="filter-result.frq" />